One possibility that I'm sure has been brought up before would be that Mace is a broken man - a Jedi who despite his virtuous intentions utterly failed to stop the rise of a new Sith emperor right under his nose, losing one of the most promising new Jedi to him in the process. Someone like Mace Windu, who from what I understand had already been hard on the edge of aggressive for a light-side user, could well be driven into full-on despair by this and react in a way similar to Yoda: retreat into exile, meditating on his failure as a Jedi and leader.
Of course there'd be other ways of bringing him back. Slept 30 years in a kolto tank, whatever. It's not impossible, but also not improbable within the established margins of the character.