If you want to ask the question of which is better as a pure style, I don't think either is really available in MMA anymore. The only fighters that are even arguable as pure BJJ are the Nogueira brothers and the only pure Judo guy I can think of off the top of my head is Kazuhiro Nakamura, and he is arguable as well.
MMA is mixed martial arts and so no one really trains in just one style anymore, but if you were asking which is better from the standpoint of an MMA fighter, let me break it down for you.
Big name fighters who study Judo (not necessarily as there primary style):
Fedor Emelianenko and Aleksander Emelianenko (it's really a staple for alot of Red Devil fighters, but it is where their takedown game is)
Kazuhiro Nakamura (probably one of the purest guys in the game)
Karo Parysian (obviously)
Big name fighters who swear by BJJ:
Antonio Rodrigo and Rogerio Nogueira (probably pure BJJ, and both great fighters in their weight classes)
Dean Lister (not purely BJJ, but probably the most notable non-MMA grappler in the world)
GSP (it is his primary form of grappling, though he is not a master in alot of opinions)
Honestly, I won't take one style over the other, the both have their strengths and they both have their problems. I, personally, study Judo, but I have trained in BJJ and have alot of respect for the guys who study it.
In my opinion, Judo is the more well-rounded style, but that is just my opinion.
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