"at the moment I'm not really thinking about adding checkpoints anywhere, but that would be a cool upgrade to add later. The hard thing with saving/checkpoints in this game is that it could remove the challenge with just being able to go to the last save. "
I thought, maybe add checkpoints in the sense of certain upgrades, if you buy them, you create a savepoint .like literal upgrades, in between that cost nothing but you have to buy at some point to reach other upgrades.
and somehow save what upgrades you have already bought including their "purchase level" (like 1/3 or such)