The only trainer we've faced with a Legendary Pokemon is N. Should there be more trainers in the game's main storyline with Legendary Pokemon to battle against, such as Elite Fours or Champions?
Not true, some of the Frontier Brains in the Battle Frontier also had Legendary Pokémon, though they weren't part of the main storyline, so I don't know if they count. Either way, yes, I do think more trainers should have legendary Pokémon. It'd be great to increase the difficulty in the game and give us more of a challenge, which is why it's often seen in hacks, and after this thing with N, I'm pretty sure we'll get to see it again. It seems there's being added more and more post-game stuff for every new game, so unless it's a rematch, I don't think it should be the champion that has one. I'd much rather see it for someone who should pose as the final challenge, just like Red in G/S/C and Steven in Emerald, so yeah.