This is more of a gameplay than a story cliché, but I really hate it when you have a party of eight, but the frontline gets wiped and it's game over. What were the others doing that they couldn't jump in and at the very least by time while I revive them? Final Fantasy XII, Type-0, Breath of Fire IV, and Neptunia Re;birth3 are the only games I can think of that don't do that.

And related, when your team splits up later in the game. At the start of them, it serves the purpose of world building and character development. Late in the game, it serves the purpose of informing you that you're going to have to do a dungeon twice when the team that the main character isn't on, smurfs up. Also someone from the B-team is probably going to die or get a booboo and be out of commission for awhile.