The resource stores are too small for the ship to function at higher levels, I lost a game close to the end because I had full energy stores but the maintenance tick happened right before automatic air refresh which drained everything in one second.
Might be solved by having the engineering and/or engine upgrades also increase the storage space for the upgraded resource by a bit.
I like the puzzle aspect of trying to figure out the route to get where you need to go, not really a fan of the fights, I felt like I was just randomly moving around in the hopes the opponent makes a dumb mistake.
Got to about day 30, my pollution rate is negative and I'm generating more resources than I can be bothered to spend. I like the idea of an incremental game where you're growing exponentially against linear costs with a time limit, but there really needs to be a way of spending resources more effectively, assuming you want to keep the growth mechanics I'd suggest 'spend x% of resources building this' instead of strait 'buy x' buttons.
You might want to do something about the layout at higher levels. The buttons start warping at higher numbers. It's especially annoying with exploits when the button suddenly jumps positions and you buy the wrong thing.
Wouldn't it be a better idea to make exploits only unlock the next one of the same type when it's bought and to have them continue indefinitely? Right now you have to scroll through the list finding those you need, then scroll back up to buy more exploit points and then scroll back down again trying to find where you left off. In addition to that the more exploit points upgrade becomes completely useless when you can already buy everything you need anyway and manually adding more exploits in updates just means it becomes useless at a slightly later point.
I think the problem is the rise prices bonus, because it affect the base pizza much more than the others it means that the further you come the more the basic starting pizza becomes better than the advanced pizzas instead of the other way around.
Maybe lower the prices of the advanced pizzas a bit and add a 'ingredient multiplier bonus' or something that keeps pace with the rise prices bonus.
The automation perks don't work very well, they're more than twice as expensive as perks that actually help you so every time I'm like "I really shouldn't be taking this as it doesn't do anything to help me and I could be taking 2-3 things that actually allow me to get further" but without the automation perks the game is incredibly effort intensive.
It might be better to make them free but with unlock requirements "You get [automation perk] for free when getting [useful thing] level X" like the first level of paint active.
I would be nice if the bulk dimboost buyer had an option 'after x dimboosts go back to buying singles'
Right now I often get stuck at points where no number really works well, at 5-10 there's a lot of dimboosts left over that don't get bought, at higher numbers I get stuck earlier due to not enough dimboosts and at lower number I lose more time dimboosting than I gain by getting higher.
I'd suggest that instead of using binary for the museum you use a system that sorts by number of mutated leaves. It'd be a lot easier to see what variations you're missing that way.