A few suggestions (and yes, I am editing this as I go):
First of all, the hamburger shop is totally broken. You can get ingredients for free. A patch for that would be nice, as well as an option to quick-build a burger or something. It would also be nice to see a greater variety in what ingredients customers order instead of just chicken, bacon, and lettuce. Also, as option to discard the hamburger that is currently being built rather than finish it. Perhaps there could be like a 50% change to get back spent ingredients this way? Also, an option to delete completed burgers, again maybe with a chance to get back spent ingredients. Also, maybe the customers could care a bit less about the order of ingredients?
Next, a quick suggestion: change the achievement for getting 10 drillioncoin to unlocking the travel agency, this way the ticket isn't accidentally wasted if someone got exactly 10 drillioncoin on their first reset, as getting the travel agency requires 11. Actually, you might want to redo the achievements entirely. You could have 2 kinds of achievements: progression achievements, which are achieved through normal progression, such as the reincarnate once achievement and other achievements that are easily unlocked without doing anything out of the ordinary. These would provide one-time benefits. Then there could be ongoing achievements, which require going a bit out of one's way to complete. The garden and gem achievements are examples of this. They would provide a lasting bonus once achieved. It would be up to you to decide what qualifies as what.
In addition, there are a few mechanics that are poorly explained. This includes item use, the magic/ability system, and crafting jewelry.
Finally, maybe add a recipe tracker for unlocked ice cream recipes in ice city. Could be useful. I also seem to be unable to scroll through orders in ice city. That can get problematic. There's also the teensy matter of practically non-existent fruit. I also think it's a bit odd that it only takes one dose of normal syrup to make 3 doses of flavored syrup. It should take at least 2 doses of normal to make 3 flavored.
Anything else I might suggest has probably already been suggested, like no having the museum reset on prestige (in order to do this, by the way, you'd probably have to make it so the reputation from the reputation sets not reset on prestige).
Otherwise, a great game! I'm not trying to point out all the faults (well, maybe I am, but in a GOOD way), I'm just trying to help point out how to make the game better.
P.S. a gem-cutter in the desert area would also be nice, don't really see why it isn't included.
P.P.S. it seems that I can't submit iron earrings to the museum, no matter if they are crafted or found naturally. UPDATE: looks like I can, there are just two very similar items, only one of which can be submitted. Might want to make "Iron Earring" and "Iron Earrings" a bit more different.
P.P.S.S. I don't see why the casino should hide your money. I can see why you might have added that, but it does more harm than good. Just store the winnings separately until you leave the casino.
P.P.P.S.S. when you pipe bomb a beam mole it's beam still says... until your run ends. That's annoying.
P.P.P.S.S.S. the achievement for forging 500 alloys doesn't seem to work. Same for the recycling achievements.
P.P.P.P.S.S.S. there's this bug, often after buying a new drill piece, where are high speeds, the game just freezes, and you have to reload the tab and restart the run. Nothing too harmful but rater annoying. Fortunately, it seems to go away after that. In my experience, you have to "shock" the game into freezing. Again, this happened most regularly when I added another head to my cyber drill.
P.P.P.P.S.S.S.S. there's this bug in the garden where after completing the fungi display (+2 days per plant), the plants will show the extra days on their seed packet, but when planted will still show the original number of days. They still live the extra days, but, for example, some of my dill says "age: 4/3 days".
P.P.P.P.P.S.S.S.S. when reincarnating you can't see how much unspent drillioncoin you have.
P.P.P.P.P.S.S.S.S.S. the sulfur trail runner doesn't show the sulfur symbol on the green box once it gets moving.