my fanfictions always involved the jedi order becoming more recluse and irrelevant while other force sects end up taking their place in terms of prominence. I went more of the cade skywallker route mixed with Kyle Katarn where the skywalker's don't really consider themselves Jedi, just people with lightsabers and lots of questions.
I suppose that with their desire to avoid a repeat of Order 66, the Jedi becoming more reclusive and keeping as low a profile as possible makes sense. Ditto with them and other Force sects setting up plenty of hideouts and contingency plans in case another Palpatine takes power or what have you. Mass-decentralization so that there's not one or two choke points for their enemies to target would be paramount to the process, I think.
I've always been partial to the idea of a balkanized galaxy in Star Wars. Though, that is something more likely to happen in the immediate wake of the ST than something further on down the line.
I guess tone-wise, what do you want to do? Straight up SW, a Deconstruction, a Reconstruction, etc? Do you want to keep to the themes and ideas of SW or do you want to do your own thing?
You know, I haven't thought too deeply about that. I suppose that making it still feel like
Star Wars is an obvious one, albeit with my own insights and interpretation weaved into the setting (e.g. long-lasting skepticism towards concentrated authority thanks to the Hitler-esque legacy left by Palpatine). To that end, perhaps something like the Old American West in space--a theme that
Star Wars already employs as is--could become a galaxy-wide paradigm that lasts for the first few centuries or so.
Technological advancement beyond just mildly new spins on basic things that already exist--blasters, droids, starships, et al--is also something I'm thinking of adding. Having super-weapons receive most of the big breakthroughs also gets old at some point, and over-emphasizes the more militaristic side of the mythos.
Honestly if your talking of a scale of millennia you should be safe to fill in much of the galaxy how you want. The fifty or sixty year portion between the Clone Wars and Vong Invasion (going by Legends) had some crazy things happen after all. Might've been the most dynamic period of Star Wars history period.
That was a point I raised elsewhere, as far as creative freedom brought about by long-term historical unpredictability goes. As per above, I'm thinking starting the first few centuries off with a decentralized, pretty much ungoverned Galaxy where people broadly distrust concentrated authority and do business without that sort of force to play referee. Such an arrangement might come with its own problems, but from their point of view, it's by and large better than even the
risk of galactic takeover and rule by an inescapable dictator on distant Coruscant. That said, their more distant descendants may think differently, since these anti-authority, slippery-slope sentiments will fade out with time.