Master Trainers are 1v1 with the same Pokemon. So for Ditto, battling another Ditto isn't going to end well. They'll just use Transform over and over until the PP runs out, then use Struggle. And basically the fastest one will end up winning. It would be a tedious battle!
As for the other Pokemon, they are legendary/mythical and there is only supposed to be one of them in-game. So it wouldn't make sense for the master trainer to also have another mythical Pokemon. (Having said that, you can find multiple Articuno/Zapdos/Moltres in the wild, so a MT could conceivably have one of those.)