Depends on what you want!
To me, Six Flags is more roller coaster oriented...high thrill rides (Titan, Texas Giant [in Texas], Batman, Freeze, etc), while Disney World typically is more "everyone-oriented" (for lack of a better term).
Rides that pretty much everyone can enjoy, decked out areas that are as much fun to simply be around and look at as it would be to ride a roller coaster (Hogwarts Castle, in general just the whole park).
Just my thoughts. =]