Normal Mawile has low attack so it wouldn't be as good as Mega Mawile, and since he has Mega Metagross he can't use Mega Mawile. Though Mawile irc was the only steel type in the dex that he didn't use in the originals (not counting Registeel), so maybe.
Actually Phoebe used all ghosts in the dex except for Shedinja...maybe she can have Banette, Dusknoir, Duskclops, Sableye, and Shedinja. Shedinja is weak though...so yeah...
He didn't use Magneton either, but that was Wattson's signature Pokemon (in RS, anyway), so that might be why it wasn't used.
As for Phoebe using Shedinja, that's sort of a bad idea. Sure, there's plenty of ways to take it down, but newer players may find they don't have any means to do so, and thus automatically lose. (Unless they last long enough to deplete all four of Shedinja's moves so it KOs itself with Struggle, anyway.)