Game's called Sins of a Solar Empire for a reasons- frankly while there are various levels of jackassery, frankly I don't think any of the factions are really someone you want running your planet. At the very least none have the local's best interests at heart as is demonstrated by each empire's refusal to capture a planet by any means besides ORBITAL BOMBARDMENT- stop and think for a moment how terrifying a thing you are doing when you rightclick that enemy planet.
OK, sure the advent Loyalists can mind control a planet, but frankly the prospects of having one's free will taken away via planet-scale mind control only sounds marginally more pleasant then orbital bombardment.
Going into the specific empires:
TEC Loyalists: The TEC have never been a tolerant bunch, as evidenced by the exile of the advent, and decades of war with said exiles and an alien race certainly haven't helped. While not as bad as the TEC rebels, living under the TEC loyalists as any sort of religious or species minority would be no joke. The TEC in general have always been big on the whole recruitment/draft thing, so you may well soon find yourself piloting a converted cargo container into battle against technologically superior enemies.
TEC Rebels: As TEC rebels only your new overlords are a Hyper-xenophobic-angry-mob....Great...just great...
Advent Loyalist: You're being ruled by a suppressive society of borg-mentality Psychics who WILL push the belief that psionic ability equals social status and anyone lackign said abilities should be marginalized until they pump themselves full of enough drugs and implants to offset their natural "defficiencies". Doesn't help that in general these guys aren't big on the whole free will thing
Advent Rebels: While not as huge on the "no free will, assimilate everyone" philosophy as their loyal bretheren, the advent rebels are religous zealots who subscribe to the "vaporize the nonbelievers school of thought". They are intent on purifying their own follower's collective conciousness, which often means expecting self-sacrifice from all of it''s members. The perfect example being the Advent Rebel's expectations of THE ENTIRE POPULATION OF A PLANET to be sacrificed when they need to melt some of the unity's enemies en masse.
Vasari Loyals: The Vasari have always been the franchises's premier space-assholes- They ruled an empire for a thousand years on military might and fear, enslaving the populations of less developed civilizations they encountered and ruling from orbital emplacements of terrifying destructive potential. Spending generations on a mad flight from sonme faceless personification of their just desserts hasn't really improve their treatment of other species. Heck, These guys are willing to consume entire planets for resources the natives be damned.
Vasari Rebels: Probably the nicest guys around these days- shocking despite the vasari's historical destestible persona is every previous iteration of the game. That said, they are playing nice out of desperation- and while they may have eased up on the slave labor, much of their other treatment of the natives hasn't changed.
Not to mention occupation by any of said factions beigns the distinct potential of orbital bombardment from they other factions.
So in conclusion Isolation is probably what's best for the locals- none of our esteemed empires really have their best interests at heart.