Nice to see this post-mortem published 
Since the first post in Protocol Development on this forum describes a recommended process for contributing to the protocol, I would just add that ultimately governance participants need to enforce that these processes are followed.
Compound III provides significantly better tooling in this regard, so the solution to (1) and (2) might be to move in that direction. A challenge for (3) is maybe finding a general-purpose undo mechanism, but I agree that it’s a great idea to explore.