First... I never even thought to hit the glass with the wrench - so I started a new game to do just that.
And laughed my arse off.
Ahem - so, yes - it's odd that Ace stops short of walking up to the door. At some point you must have clicked the hand or the walk icon on the door - to make Ace step forward, to allow him to interact with the door controls.
As for the close up of the bolt in the vents - you need to be standing close to the vent to get that screen to appear. If you're standing away from it, it will just give you the dialogue about the bolts. (I am assuming because the game wants to tell you that you're not standing close enough to see the bolts - similar, I suppose in real life, if you're not standing close enough to a screw in wood - it might be difficult to see).
As for Rooter, once he's on the other side - switching to his "nose" icon - should have allowed you to click on the controls.
As for the items on the desk - yeah, I actually like there's no "hot spot" where your icon tells you something is here to do. Yes, it may be tedius to click and drag every item on the table to just see if it moves - but I think that sort of helps make the game a "just move the cursor around until it turns green" - because that'd seem too easy.
Now granted, several people have mentioned the UI being clunky. I've now played the game (as far as I can) like 15 times now - so even the walk through I wrote may be making too many assumptions based on my repeat plays to keep trying to find odd bugs. So if something's not clear on the Walk Through, by all means, reply in that thread and let me know and I'll update it.