I'm basing this off of what I've done...been to three parks from each chain (Cedar Point, Kings Island, Carowinds; Six Flags New England, Great Adventure, Over Georgia). I'll say without a doubt that Cedar Fair is the better chain. Cedar Fair parks are just much more enjoyable for me, for many reasons.
The staff are much better than Six Flags, in every way shape or form. They are friendlier, more efficient at operations, and more disciplined. The staff at Six Flags are a big reason why I'm not a huge fan of their parks. I've had encounters with SF staff that have left me annoyed or unsatisfied... they're really just there to "get the job done." At least Cedar Fair staff actually care about what's going on, and in the past I've had some pleasant little conversations with them as well.
Cedar Fair parks are also just a nicer places to be in. While neither chain focuses a lot on theming, at least Cedar Fair presents their parks pretty nicely. The landscaping/foliage/etc is much nicer compared to the Six Flags mindset of buildings and rides placed on concrete (more or less). Look at the recent Cedar Fair coasters: they all have cool plazas that dominate the ride's area. They'll include gardens, plant trees, maybe even design a cool station. With Six Flags it's just plop down a ride, put up a big tacky sign and that's it. There's no character.
Then obviously you got the investment conversation. Both parks love investing in rides, but again Cedar Fair wins here. They may end up giving some of their parks jack ****, but that allows them to invest in one (sometimes multiple) $25 million ride every year. Six Flags likes to spread the love and get something new for all their parks every year. That's a fair approach, but then you end up with stuff like S&S free spins, Larson loopers, and pendulums at every park, which people (at least enthusiasts) are sick of by now. Meanwhile Cedar Fair are pumping out Furies and Steel Vengeances. I'll give Six Flags the RMC's though, they've done a good job with investing in them and they're the perfect ride for them, given their financial situation. But overall, I'd rather have a chain go all out on one or two of their parks and invest in major and unique rides, rather than a chain half-assing investments on a bunch of rides that all kind of blend together.
So it's not even a question. Cedar Fair is the better chain, at least in my experience. I can't speak for the lower-tier Cedar Fair parks, but I still think I'm more interested in visiting a California's Great America or a Michigan's Adventure than a Six Flags America or a Great Escape.