I might give rebellion handling another look when I return to Nex work.
Just to add my two cents: my experience with them is limited, since my current one is my first really long campaign with Nex so take this with a mandatory grain of salt, but I've definitely had a few rebellions that won in my sector. Mostly in newly founded colonies at the fringes of the sector (where suppression fleets might have some troubles getting in time/safely), but I've even seen Oasis flip because of one (in my game Oasis has a tendency of rebelling because of a Kadur Remnant pretty severe stability malus).
Personally, I would
not want to see rebellions succeed more often than this without player intervention. I actually like my Nex universe to be slower than it currently is (not necessarily more static, but surely slower in developing and flipping colonies left and right), which is why I've myself edited it to have weaker and fewer invasion fleets, slower colonization etc. This is because I like having the chance of being somewhat in control of the sandbox (so, for instance, I can take my sweet time in the early game without having to run everywhere to save some weaker faction that would get swallowed in the first cycle etc), which is impossible with the default settings. So,
fewer rebellions that might have a bit more chances of winning? Maybe, but sure enough I wouldn't simply want them to only have more chances. Or, at least, I'd ask to have a corresponding value to tweak in the config file, so I could tone them down to my playing pace.