Well, SEGA doesn't have a problem with fangames as long as there's no chance for commercialization (and thus potentially driving away sales from SEGA).
You can still sell GPL licensed works though.
So the real issue is: If a game uses Sega-trademarked content and is being sold - It's is an entirely different issue that doesn't have anything to do with the engine you use to make said commercial Sonic game. If anyone *sold* a Sonic game made with CryEngine, Unity, UDK, Adobe Flash, HTML, EggEngine, SonicGDK, GameMaker, or even BlitzSonic there would be trouble, regardless of whether it's a custom-built GPL engine or not.
I don't see any problems with a permissive BSD/MIT/ZLIB license because there's no trademarked/copyrighted content in the graphics system, collision system and physics system, or engine itself.