I'll start:

Twilight will obviously main Female!Robin if players understand the meta information. Plus, they have very similar personalities.

3682111 I see Rainbow as either Fox or Sonic. Maybe Zero Suit Samus. Regardless, she would be a fighter for fast movement and quick strikes.

Applejack would be comparable to Little Mac or Link. She's quick enough to be a speedier character but I think her strength would be in...well...her strength. If not one of these two, someone who is semi-fast but packs a decent wallop.

3684361 Lucario sounds good, but I think Ike may be too slow.

3684372 Yeah.

Fluttershy would main Villager because he's a very unconventional character.
Rarity would play Zelda because Zelda's fabulous.