A lot of this is great, but base building fundamentally doesn't work as a prestige mechanic because your reward isn't based on the content that gets reset, its progress is almost entirely independent of the main game.
Also you can cheese a lot of things by toggling core upgrade option things. Like switching to active ability duration/cooldown, activating active ability, then switching back to the passive boost. Or switching the beam from ramp up to power if it's already targeting something.