They're both superior in quality.
Frank Zappa is without a doubt one of the most influential progressive rock/psychedelic rock/avant-garde musician of all time (well, was). Luckily we have Dweezil to carry on that genius. Unfortunately, when people think of Floyd, we don't think of comical music that was released by the likes Zappa.
Overall, I prefer Pink Floyd but I don't understand why we can't enjoy both bands equally. Unfortunately, I can't - I need to be in a certain mood to truly enjoy Frank Zappa's music, although I always enjoy his primarily jazz fusion albums.
Edit: It's funny that you think Roger Waters and David Gilmour could simply "beat" Zappa in a guitar battle. Truth is, Zappa is one of the greatest guitarists to ever live. Although I prefer Gilmour as a guitarist, I believe Zappa would come close to Gilmour; Waters, on the other hand, I believe, would get his as* handed to him.
Everyone's opinions are different. ;)