No, for a few reasons:
1. The Company is one of many places the Organisation sources its resources from, and they wouldn't have been significantly impacted by having this one route cut off.. After all, it would be lunacy for them to put all their eggs in one basket.
2. The Chief makes it clear in the confrontation that he's been planning this for a long time, so he would have prepared for, and planned around, the MC controlling The Compnay.
3. Cutting off one source of resources doesn't instantly disappear all the existing resources.
4. MC was concerned with keeping a low profile, so it's unlikely he would have closed off The Company's supply chain anyway - that would have set off MAJOR alarms within the Organisation (although unknown to him, they already knew).
5. MC can't use the smuggling/mercenary supply chain himself, as again, that's linked to The Organisation, it would have been extremely obvious, and he wanted to keep a low profile. Where would he even keep mercenaries?
6. MC wasn't expecting to go to war - quite the opposite. He was hoping to quietly infiltrate the Factions with the aim of remaining safe while he figured out the various mysteries confronting him.
7. As for the Fey allies, again, he was trying to keep a low profile and sneak into the church. Bringing the Fey into the Organisation-monitored city would have been catastrophically dumb. And they wouldn't have known themselves, as Morgana was obviously playing a solo hand.
In short, MC had no reason to build an army or bring numerous allies with him, and in fact it would have worked against his desire to sneak quietly into the church and keep the factions in the dark about his plans and allegiances. In hindsight it was a bad idea, but MC had no way to know that going in.
Mechanically, also, what you're asking for is a completely different Act Three based on choices made in Act Two. Which is something even AAA studios don't do, so a solo dev on a weekly schedule attempting it would be near suicidal ;)
As for MC owning everything in town:
1. Buying and upgrading each store wouldn't significantly help the MC. The income from most of them would be miniscule, the benefit dubious and with every purchase it becomes more obvious what he's doing.
2. You literally can't own governmental institutes. MC could attempt to, eg. Shatter or Awaken the Chief of Police but the police are obviously under the Organisation's thumb (hence the Org just staging a kidnapping and assault in the middle of the street) and so any attempt to control them would run an extreme risk of being noticed.
3. Fire Department would be an odd choice of target. MC isn't looking to hold the city hostage. Hospital would be a kinda decent option, but wouldn't really give him anything he doesn't already have (it's not like they'd refuse to treat him if he just walked in, the Org have their own doctors, and the Fey/Eldritch don't use them).
4. MC was interrupted halfway through his plan. It's likely he would have taken over a lot more properties, but he wasn't given the chance.
5. MC had only just finished framing Tom when shit went down, so didn't feel secure enough in his position to start snooping around potential Org sites. He almost certainly would have, once he felt he was safe, but again - no time.
And - finally - remember that the MC isn't perfect. An outside observer with time to consider and without their life on the line would no doubt have made different choices, but that's not the MC. He has made mistakes and will continue to do so - it's a function of being human.
Whew! Quite the essay! I apologise for the wall of text, but I hope this answered your questions :)
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1. The Company may not be the only resource the Organization had access to but it is for this Town (the rest of the world I can understand). Lets not forget the 2nd Branch Office isn't exactly what they would have liked and didn't want/fully prepare to have to use it.
2. Yes I get the Chief has been planning this and that should have been a thought for the MC who is overly paranoid. The Morgana assisting em may not have fully crossed his mind. Not to mention what coming into contact with the Relic near the end along with Morgana control of the Artifact.
3. While cutting off one source of resources doesn't hurt em but it does hamper em if there are no other sources within the Town (it would take a bit longer pulling sources outside the town and can be a bit more notable for other parties to see not just Morgana, the MC, but other Organizations and possible Bodies that don't agree with how this Organization works).
4. I wasn't referring that the company completely close off the supply chain. Just make the process slower which will mess with scheduling and forcing rerouting a stock from other places. Only close it off completely when it is time to push back.
5. The Smuggling of supplies can be tampered, screwed with, or even outright sabotaged. Mercenaries don't always have to be connected directly to the Organization because will they are mercs. Mercs normally have little to no connection to any Organization and do what their paid without knowing who is or what is giving them their money (yes there are mercenaries with an alignment code and some that require more information then just a basic attack dog but would those mercs even willingly accept working with the Organization).
6. The MC at the start of the game wanted to completely get revenge on the Organization for his mother's death. Most revenge concept follow with a secret war at one point or another. Let's not forget how badly he got captured the first time. Backup plans and not fully going it alone should be on his mind not to mention to better equip himself and those following him.
7. The Fey wouldn't be the entities from the various planes technically don't really count since they don't follow under Earth standards or obey Morgana (Hell the organization has no full knowledge of the Nexus and the worlds the MC has access to). Not to mention they just have to hide out in the Manor. Speaking of which since the MC was able to make a secret tunnel at the Marina making tunnels connected to various things he owns would allow for the Organization to not know anything that happens under their feet. Not to mention if Ami followed the MC stealthily why wasn't Molly there to also act as a backup assisting Gwen? Lets not forget the Magician girl and her summons (the organization doesn't seem the type to have actual magic users relying on mostly tech if I can remember [It would have also been nice to have the option to invite her to the Manor and who knows she could have known a spell to seperate and not harm Hana and Ard allowing them to have their own bodies because Alchemy/Magic]) and her magical expertise could further MC and friends a favorable boost in things magical and enchanting.
8. Buying and upgrading businesses. Having a Security Firm created outside his name under someone he turned into a follower (For example Molly who the Organization has no knowledge of). Acts both as Intelligence gathering (by putting up Security Cameras) and depended on the businesses (The Club bouncers and Stores basic Security Guards) keeps Organization loitering in places down and out of certain areas they shouldn't be in (creating blind spots with no person or their technology can be). Let not forget when acquiring the University the relationship he built with Veronica and her mother (can't remember her name at the moment) why he didn't coax them to let him acquire their home as him being a part of their family and wanting to protect em (This allows for more space when moving allies and possible allowing for the investment of making a tunnel between the 2 Manors).
9. True you can't own Government buildings but individuals can owe the MC favors and while you say the Organization holds the Police under their thumb. Things can change if the MC turns the Police Chief into a Secret Follower (or if that isn't possible grant him/her another option) not to mention by your own words the Police aren't willing participants. Throw in the fact the MC could also donate a huge sum to the Police Departments which could greatly increase the number of Officers in town but also better equip em (along with the company further supplying them secretly with misplaced resources from the Organization [as certain Merchants in games say just stuff that fell of the back of the trucks]). Having a few officers with a bone to pick show up around the church. Seeing a bunch of Goons in suits with guns aimed at mostly unarmed possibly civilians (lets be honest not all the officers would have knowledge of the Organization just the higher up being threatened when they didn't have the proper backing to bite back).
9.5 Yes the organization does have their own doctors but other then the Branch building in town (which is pretty small) they would have to go out of Town or go to the Hospital. The MC manipulating Branch Leader's daughter just enough and promoting her desire not to be there (along with a few devices to malfunction recording devices). Say the chief isn't in the Branch Office and most of the guards will be gone for awhile (she supposedly stepped out and mysteriously a fire broke out not that she would really care).
10. A difference in timelines not that much. The affects of the Relic (whether he took it or destroyed it) and Morgana's control of the Artifact. He could still technically pass out and be in a coma for 3 months (considering the whole original factoring that slowed it was he was on a major adrenaline high keeping his body from registering the crazy shit happening inside him and him summoning the Entity [If it was more favorable he wouldn't summon the entity he would have come off his Adrenaline high sooner and passed out from the crap from the Relic and Morgana's pull on the Artifact]). The big difference is how bad the Organization walled off the Town and the warzone to some degree inside (how much it favors his side or any of the others).
11. I know he wouldn't be able to pinpoint everything about the Organization (especially anything outside the Town) but inside Town it was already considered contested before the MC arrived. The destruction of the first branch and when the time is right everything inside the town that was under the Organization ripped from their control (they would have to rely solely on pulling everything from out of Town and that takes time and more manpower to get a proper and reliable supply chain).
Finally yes the MC isn't perfect but learning from one's mistakes is also human. The situation at the end of ACT II has similar feel when he was captured and held hostage at the First Branch (never trust the Organization which stands to having a number of plans for when their going to screw the MC over and never have too few allies when it is possible that shit is about to happen [as stated were is Molly and other eligible individuals on standby to assist Gwen like the magic girl and hell even The Club Girl could be called in since she also has a beef with the Organization and knows how to fight] and never trust using the Eldritch Entity maxing his stats should have given insight to have prepared other contingencies for the overly paranoid).
Lets also not forget that the Branch in town in Undermanned. Focusing what manpower they have to keep an eye on the MC while Tom escaped and was able to make it to the Church. Don't forget the Goblin Girl wondering around in Town in her human suit proves they are having difficulty noticing things. Lets also not forget there was only 2 Guards at the front of the Church when stakeout scenarios would have at least 4 - 6 making the MC require to do more stuff to fully distract all of em (This is taking into account police and F.B.I. stakeouts).
Speaking of the Main Branch Building and surrounding compound in the Town. While it is true the higher up in the Branch Office would be able to gain special living conditions the lower ranking would require whatever they can get their hands on (when the town is walled off they can have tents, makeshift buildings made, and make use of Trailors) but if the MC was able to purchase any Apartment Complex, Hotel, and Motel he could put a damper on those sleeping arrangements were once maybe 2 Goons may have to share space now they are forced to share with maybe 4 or even 6 sharing the space. That creates problems (Friction and Exhaustion not to mention if any infighting).
Speaking of the Ambush there is also the Ninja group the MC could convince to assist him (they can use the Tunnel to get into the Town). Maybe not be at the ambush but convince them to attack a weakpoint (most likely a structure at one end of the Town) which will force the Branch Leader to send Goons to fix it reducing numbers at the Ambush site. The Goblin Girl could be convinced easily (allowed to set something on fire or possibly blow it up) to destroy an Organization Warehouse in the opposite direction and get out of there (that will also deviate goons from the Ambush site).
You are assuming a LOT of things either not in evidence (that MC has the slightest clue about subtly tampering with supply chains), that are actively contradicted in the story (that The Company is the Org's only supply chain point when we know the Marina at least was another one) or that are factually wrong (MC out on a personal quest for revenge to find the person responsible for what happened to his mother has to lead to WAR).
There's a lot of other points that could be gone into where you've misunderstood MC's motivations (investigating vs toppling shadow empire) and think he should be behaving more like a spec-ops commander, or have gotten aspects of the geography and suchlike wrong (the tunnel doesn't lead into the city), but everything salient is covered in my original post.
In short, everything comes down to the question of: did the MC behave in a way that is believable for his character as demonstrated throughout the game? I would, of course, argue yes (he's got a certain amount of cunning, and adapts quickly to new situations, but he's also kind of a dummy). If you disagree then that's a shame and I hope you can look past it and enjoy the game regardless. If not, that's okay - it's impossible to please all of the people all of the time, and fortunately there are so many awesome developers working in this field that I'm sure you'll find something more to your taste.
In any case, for any further questions on this topic, I refer readers back to my original list so that this doesn't turn into a one-hundred page dissertation ;)
Sorry. There maybe parts of my memory that is incorrect. I may also be injecting my own personal experience of having been jumped by groups of People for "That white boy is different" and have been beaten near to death in Pre-K leaving me in the hospital comatose for several weeks (the doctor telling my mother I might not make it [it is all in the paperwork]). I have developed P.T.S.D. over the years and that was before I had joined the Army. People do not get over it and I was projecting elements of my experience on what may the MC had felt. My bad.