Trixie coming back isn't that hard to come up for an excuse for. Off the top of my head she comes back to Ponyville in an attempt to redeem herself. And I don't mean saying sorry, but coming back to prove that she is the Great and Powerful Trixie.
For Discord what I would love to see is how he was originally defeated by Celestia and Luna. If they were to make a MLP FIM movie that's what I would want it to be.