This is an awesome idea! Combining tabletop turn-based Pathfinder goodness with some Civilization-esque kingdom-building and technological rediscovery, with a bit of Rogue Legacy with passing character stats/gear/progress from generation to generation... this is pushing a lot of my "like" buttons.
I don't think I'd ever run this system; not sure if I'd even play in it. I just don't have the time to devote to a system this complicated; definitely not during school. Still, this sounds great!
Oh, right, how to improve it. Well... it'll take some time for me to run the numbers to see how fast/slow the game progresses. The "NPC classes only, almost no gear, almost no bonuses" start seems painfully slow, but I'm more used to mid-level play. Besides, anyone rebuilding civilization has got to start somewhere, right? Other than that, no real problems I can think of!