I really like the idea of completely different themes for each restart, it would keep the game much more engaging than the basic start-again-a bit-harder setup, but I don't really see how it fits in with the basic premise of the game you posted earlier. I'm sure it will be more clear when the story is finalised.
I do hope that it would be a bit customisable though, like you can blacklist certain options. I really hate mob wave scenarios! The cave in one sounds really cool, though I'm not sure how you'd start your second generation in that situation.
Are you going to keep the current Champion-Elite-Legend-Ultimate difficulty levels? It might be nice for people who like that sort of thing to be able to apply the difficulty modifier to any level of character when it is unlocked.