I am also a player who often stalled out in the mid-game.
I'm also a really big fan of alt-win conditions, especially as you've implemented them before - the Fallen Spire and the Exodian Blade were both fun win conditions to chase.
I do think it's important that different win conditions use different resources, both so that they play differently and so that the player doesn't get locked out of all of them by the same mistake or the same lack of interest. For example, if all the alt win conditions are hacking-based that's going to be unfortunate if a player doesn't really enjoy hacking that much.
I do like the "hack the nanocaust" win condition. I also like the idea of a "turtle" win like the showdown devices - maybe "build, protect, and fire a superweapon" of some kind. That could even be a "soft win" condition. For example, it could be a Sins of the Solar Empire style superweapon that gives the player a massive edge in hammering the AI but doesn't instantly win the game for them.
Another option might be that there could be fragments of alien supertech on certain planets - sorta like Ascension Crystals from GalCiv - and capturing all of them nets you a win (maybe after holding them for a certain period?).
I would really like a Fallen Spire-style "summon bigger fish" win condition to still exist, though.
Involving the Ark in a win condition would be cool. Oh! You could have a Mass Effect 2 style win, drawing on the old Nebula missions from the AIWC. Some kind of mission you can send the Ark and a limited strike force on that wins you the game if you win, but it's a one-way ticket; you lose the Ark if you fail. Would be particularly interesting if, like Mass Effect 2, it's something you can attempt reasonably early but will certainly fail, so it becomes kind of a game of judging when you are strong enough. Could be another place to implement a "soft win" - like for example the thing the Ark does is destroy the exo-galactic relay, preventing the AI from getting reinforcements (or severely limiting their reinforcements).
EDIT: Can the ascension crystal style win condition be "take control of the Astro Train stations and make those bastards build
you a superweapon"? Please? That would be so satisfying.