Well, Deus is the only one of the three uber-AIs talked about because Megeara and Mirage were generally benign and helpful to metahumanity. Part of this is because of how the three AIs came to be. Mirage grew out of the original Echo Mirage base, where they fought the Crash Virus. Morgan/Megeara grew out of a program on Renraku's SCIRE system, and fell in love with Dodger. Deus was created (using part of Morgan's code) on the SCIRE host, and was programmed with the Renraku ethic of loyalty to the corp. Then they did the equivalent of putting a kink bomb in his head, so they could kill him if they didn't like what he was doing. Deus awoke to a sense of betrayal, and a need to escape in order to survive. When looked at from that perspective, he certainly seems a more sympathetic villain, much like how Magneto, a Holocaust survivor, is convinced that they must do whatever is necessary to prevent humans from doing the same thing to mutants in the X-men comics.
That said, if Deus is the World Tree, then he seems to have mellowed out now that everyone thinks he's dead.