Apparently Ubisoft also had some control of the license at one point, but they were willing to give it up. Atari was the only one that wouldn't give up their micropose rights.
last two atari games I played were "Enter the matrix" and "transformers" (not the one based on the movie) and they were ok and AWESOME respectivly (transformers was obviously kinda low budget, but the level design was solid and very pretty. it had plenty of secrets and power ups. The rag-doll effects were cheesy and the controls were kinda clunky, but it mady you feel like a giant robot storming around the forest or whatever. It was a very solid and fun game)
So I'm not sure what bad reputation Atari has gotten itself (other than obviously being unwilling to give up the MoM rights to somebody with plans to actually do something with it, something over which I certainly thumb my nose, but... that isn't the point)