Okay so this is just a suggestion, please don't hate on me for it
But I'm thinking maybe some of the blocked structures could be re-enabled with insane crafting costs. I'm talking one of each alpha boss trophies for a nanny or mutator for example (a bit extreme, but again it's just an example).
As the vivarium and tek fridge proved, changing crafting recipes can help with either making it easier for players to get stuff or much, much harder. This way, players that are at the end game could lessen some of the grind, and give them something else to strive towards.
But again, this is just a suggestion. It sounds good to me, but I'm sure you guys have great counter-arguments that I can't wait to hear.
EDIT: Also the mutator could be enabled as a buyable event. Kinda' like the scanning event, but for mutations. All of its functions can be disabled via the ini, making it basically a decorative structure outside of the event. But that's just my two cents.