Maybe while being teleported back to Gallifrey something went wrong because of him being skeletal or whatever that was, maybe something like when the TARDIS tries throwing Jack off in Utopia, and the Master ends up stuck in the Time Vortex and the Doctor needs to save him?
Useful foil the Time Vortex
I have to admit I was never convinced the copy we saw get zapped in with the Time Lords was actually the original. I had some bizzare notion that he got to Donna ( don't ask me how) and is being hidden again.
Lame I know but it was my way of getting Donna back too
I'm not sure they should bring the character back to be honest. I have only seen Jacobi/Simm and Delgado and while I thought Roger Delgado was absolutely brilliant in the two stories I saw, Simms master seemed to go horribly wrong. They should only bring him back if they can restore some of the greatness that the Master had throughout the Classics, otherwise they should leave the character be
I think it's safe to say that he WILL be back - it's more a question of when and how. If it's Simms Master you have the problem with then I wouldn't be put off because aside from shooting a regeneration scene I doubt Simms will be that involved. And as we know The Moff has a very different take on things to RTD.