Mhhhhhh... in that case we'd be essentially talking about a Spore like approach. You start as 1 planet 1 /custom designed\ explorer ship (and maybe the first localized terraforming and mining attempts). Due to movement issues you'd have to do a sort of mass effect approach to travel though. Maybe by limiting quick travel possibilities to energy output of a civilization and only on very narrow paths (with many other stars relatively close by that can be reached by "standard" travel)
Outside quick travel network colonies would remain small and stagnant hubs of criminals, bounty hunters and grey-businesses (but there'd be many story possibilities with that.. border worlds and such ,p)
While main-route planets could be developed sufficiently faster and thus unlock the next gate. Obviously similar to Mass Effect there should be a reason for these gates, and it might not have to be a good one.
That way you could balance progression and spread so each empire is about the same size (but with extremely random "side" worlds off the beaten path giving them specialization tech access. Because I find is unrealistic that research would progress differently for other species just like that. The "stone age to space age" transition must be nearly identical for any intelligent species. But in space age, remnants of old death civilizations or rare alien plants/bacteria/species we find at remote locations are likely gonna be far more important. And this could be used to guide empires into directions (randomly, obviously).
3rd Stage would be Empire stage with the central location being the council world (as lame as it sounds) again, lots of story possibility. And 3rd stage is when 1 empire gains supremacy in some way, the game would do a realm divide to unify the galaxy and/or face the plot threat.
Essentially, we'd be talking about at least 3 distinct game stages. A concept no 4x game ever even attempted by the way. And if moddability and scripting is strong enough, side worlds could be seeded with random RPG like missions. And maybe even an "immortal" player avatar so that we can get immersion into the whole thing. We could be playing the first mobile quantum AGI platform in the shape of a human or other shapes we could choose (robot or even animal like body). When money is abundant.. walking around space stations or on locations on planets would be awesome too.
I think for a 4x game to be really successful it has to actually allow you to experience the empire and see how it changes as it grows. Or see what is wrong on a certain colony, talk to people there or experience situations or plots that pop up. There could be done so much with that (Cowboy Bebop and Ghost in the shell united ;P)
Like you say Cyborg, every system in a 4x game needs to be taken at face-value, re-examined, re-tooled. Needs to be immersive, fun and interesting, but also somewhat complex and easy to *understand* and control.
There also needs to be some way to make these things not all happen in 1 game.
Heck, if we are crazy why not change the "uber-plot-end-game thread" and have at least 3 or 4 different end situations that are vastly different. With different goals.
And imo, race interactions should become more advanced too. There should be options of symbiotic alliances. And these should be emergent situations. So not predictable, but when there and the player likes it, extremely satisfying and deep.
I feel like we are describing like 3 games here. But it can be done. Someone just needs to have the intention to really shake this genre.
And just thinking about it, even the start premise (the *reason* of expansion) could be vastly different, we could even do "dieing homeworld" situations or "safe us please" or the like. Or we could play an empire under an symiotic (good or bad) situation either playing within these boundaries (a sub-empire?) or trying to break free and dominate the other empire...