I had a really good time with this - I may well break my usual rule that incrementals are a cash-free hobby for me. Chapter one is a pretty good tutorial, and chapter two develops the mechanical themes in a good direction. I like how seamlessly you move from flailing about clicking random buttons that obviously aren't getting you anywhere to meticulously planning a hand-crafted route to exactly where you need to go. I was at first confused about how you could possibly reach the harder of the two endings on chapter 3, but that just made working it out that much sweeter.
I will say on a negative note, I'm not sure the prestige mechanic is adding very much to the fun elements of the gameplay loop. I think not showing which actions unlock new actions until the second run through a chapter is good, but I think time warp should maybe be the default for actions you've done before (or, if not x10, maybe x2?). And the extra mana and power can really warp chapter 1, but by chapter 2 it's already almost useless. I honestly think this game would work okay without a prestige currency/mechanic, but if you really want to keep it in maybe it would work better for the prestige currency to unlock certain action branches? Like, maybe in chapter 1 you can't study the stone until your second run through or something? Just a suggestion.