You've got a great game going here. A couple of things though. The autopause after getting wiped is annoying (though there's no autopause if you die in chapter 1, oddly). It's also possible to soft lock if your last check point is too difficult for the one zombie you start with. The game should put you back a couple of stages before your last death at least and get rid of the autopause. That would prevent soft-locking and enable AFK farming.
The "AFK upgrades" seem crazy expensive for something that resets on prestige. It would take several days just for one of them to pay for itself. It makes no sense because of the prestige mechanic.
"More points for highest wave reached", like others said, it doesn't feel great if it's all-time highest wave. More points for highest wave this run would be more balanced and rewarding.
I tried the desktop mode during the tutorial and had trouble changing it back. It's a neat feature, but it should be easier to get back into full screen.
The "Mutant Strain" costing 10 mutation points and then resetting on prestige is horrible, considering how grindy the points are.
I brute forced my way to 55 using an autoclicker to buy the zombies.
The balance in this game just feels wacky. i.e. the entire passive tab should be like 100x as powerful. "+1 brains on new run" is stupid for what it costs. Mutation points should increase at higher waves. I seemed to stop getting them after wave 50 with 29 pending mutations.
Purchasing "Alpha carrier" didn't update for the current run. Guess I need one more prestige. I wish the description said "brute" instead of tank. I thought I was getting a special zombie type. This upgrade is very overpriced considering the current gameplay loop.