What I think is gonna happen for SE is the FIRST time you play it, you have to go according to story. Which includes unlocking people, or "recruiting" them to your party as you go along. It seems that before each stage, you choose which number of chars based on the stock for that stage. For example, say you start as Mario, and you've met up with Pit and saved Zelda, and the level you are about to do has 2 stock. You then choose the combination of 2 people for that stock, and when your first choice dies, you become the next one.
What this boils down to is, when you've recruited everyone you can for that play-through and beat it, you restart SE and already have everyone on your team from your last play-through, but still have to recruit the chars that cant be gotten all at once, like Peach.