1. Yeah I agree, I'll need to tone down their spawn rate, especially space elevators. I'm still thinking about the possibility of dismantling megastructures. I guess it doesn't hurt to add the option and not force the player to explore more after seeing an undesirable megastructure.
2. Normally I addressed this bug in v0.26.1, is it still not working?
3. Yeah definitely. Though I think upgrading ancient structures should at least be gated by dimension stuff. The ancient shipyard as you described definitely isn't working as intended, do you remember how you sent the ships? (standard drive, plutonium drive...)