Some glitches/ideas regarding the new features:
1. There are too many broken megastructures, disabling the terraforming of otherwise valuable planets. Even that aside, it would be nice to have the option (either by default or as a tech) to downgrade and dismantle megastructures (or even gigastructures for that matter).
2. When encountering a level 0 broken megastructure, I can't repair it. The tooltip says I lack the technology, which I clearly don't (unless there is a hidden tech somewhere).
3. The ancient structures on the planets could be upgradeable and dismantleable. Also, the home planet's ancient shipyard seems to give XP to my ships regardless of where they are. Very nice as I hated the previous versions' battle XP grinding aspect, but maybe not working as intended.
As a general summary of the above, I believe that by late game, having become the leading star empire in control of entire superclusters, I should be able to do with structures what I damn well please. :)