The theming of all the mechanics is excellent. This is probably the first time I've seen a prestige and layer 2 prestige themed in a way that makes sense thematically. Usually it's just a prestige and then a super prestige with a lot of handwaving away of why certain progress gets wiped and some don't. But here you tie it in with the time mechanic and it makes sense what the difference between a loop and a reset is and does for the player.
The 2 gameplay phases help a lot for gameplay, giving the opening sequence a whole lot meaning, and also making perma-upgrades/perks enticing to get because you actually have to figure out a good sequence to obtaining them.
I didn't understand the reason to time travel only halfway back, was it always best to just start over from the beginning? If there is, then that's yet another unique feature you have here, which is the idea of a partial prestige.
Really good stuff here! You have a lot of different systems but they tie into each other in a complete way. It did take me a while to figure out what I was doing but I'm glad I stuck with it.