Dropping 6 Flags makes the most sense to me since it’s an antiquated name built around a series of themes that really no longer exist in any of their for a variety of reasons. What would be the point of renaming the parks “Six Flags over Sandusky” or “Six Flags over Buena Park” when these parks still have their own unique themes and cultures?
The "value" of rebranding would definitely vary. There's no benefit of attaching Six Flags to the CF parks in Ohio-too many toxic associations with the failed Geauga Lake. In markets with current CF and SF parks close to each other, like SoCal, NorCal, and Virginia/DC (assuming they're allowed to keep both parks in each scenario), branding the CF parks to Six Flags would just create confusion.
But if they think Six Flags Valleyfair or Six Flags Michigan's Adventure will result in an attendance boost, they may well do that. It's not like those parks are in line for a new coaster anytime soon anyway-so if they can get a buzz by changing the sign out front, I imagine they'd be tempted to do it.
My only speculation on the Warner properties is if they aren’t in active use will the new combined company see value in keeping them or would Warner prefer to get these domestic theme park rights back?
I don't think Warner Bros. much cares about domestic theme park use of its properties. It has started or been attached to-but since been extracted from-parks or park chains in the US, Europe, and Australia. So I think the interest from Warner itself, in terms of them wanting their own properties for a park of their own, and assuming things stay as they are now, is non-existent.
Now, if WB merges with Universal, that's perhaps a different story, but I'm not anticipating that for a few reasons:
1.) The existing Marvel licensing agreement in Florida is beneficial for both Disney and Universal. I don't feel like either company is eager to change the arrangement that stands, nor would either company much benefit from such a change.
2.) DC (and Looney Tunes) have been associated with Six Flags for so long that I don't know if, say, USH would benefit from trotting them out on its own property. Not quite the same situation, but it reminds me a bit of when Cedar Fair was going to send Demon Drop from Cedar Point to Knott's-only to receive an onslaught of pushback from Californians that they didn't want Knott's to get a ride that Magic Mountain had not only had for a long time, but had just removed. I feel like it would result in, for lack of a better term, a sort of 'branding dissonance'.
I expect there's a decent chance Looney Tunes would be dropped after the deal goes through, but DC has done good things for Six Flags over the years. Then again, old guard CF leadership ditched Nickelodeon when they had the chance to renew or expand its usage, so perhaps they'll do the same this time too.
Would it have been better for Disney to buy Knotts from the family instead of Cedar Fair?
Doubtful, unless you believe Knott's Berry Farm as it exists today would be improved by, say, turning the Calico Mine Ride into a slow dark ride version of Seven Dwarfs Mine Train.
Whether the park was sold to Cedar Fair or Disney, sooner or later it would have been mucked with.