I'm not sure what the game's developers have planned for the base game, but for those who want an extra challenge in the latter stages of the game, IE colonization, I think it'd be really cool to add in some kind of veritable existential crisis that you actually have to worry about. IE, [REDACTED]
[REDACTED] Form their own faction once a certain conditional in the game is met, IE level of the player or planets colonized by the player. Perhaps it's triggered when the player finishes a certain story mode mission. Once [REDACTED] establish their own faction, they start invading and bombing every other factions planets indiscriminately. The job of the player is to mitigate losses as much as possible and work with the other factions to stave off the [REDACTED] threat, until the [REDACTED] Faction is eliminated. This way, there actually is a way for the player to well... lose the game, if in fact all the other factions are erased. If you aren't prepared for the threat, you're screwed, and you have to try again and learn what you did wrong.
I know a lot of people have already pitched this idea for the base game, but I think a mod might suffice for the interim. Just a thought