I've reread the 13th book last night, and I don't know, I just thought about things up. Man, I can't help feeling sorry for the Bird-boy...
Anyway, Tobias actually wanted to become human and retain morphing power, that was what he wanted.
However, as morfowt pointed out, the Ellimist said:
"AND WHAT DO YOU WANT IN RETURN?
"Well, you know..."
YES, BUT DO YOU KNOW TOBIAS? AND IF YOU HAVE IT, WILL YOU STILL KNOW?"
Tobias thought he wanted to become human again, but later in the final chapter of the book, he realizes that life as a human Tobias sucked anyway. No cozy bed, no delicious (but still easy) breakfast... the only thing he would gain from being human again is Rachel and the others. He was just satisfied in gaining the morphing power back... sure, the "Ellimist" "cheated" him, but he couldn't do anything about that.
Tobias, suddenly being in his room again, back in time, was just a bonus. I guess the Ellimist thought that what he did was fair enough, and gave him a chance to become human once in a while. That way, he would always be anything he wants. To be a hawk. And a boy. I think he got what he wanted.