While the Mario RPGs do have partners, having enemies as "pets" is very uncharacteristic of the Mario series. This idea sounds a lot like Dragon Warrior Monsters, Pokemon, or Keitai Denjuu Telefang.
Partners would be cool, but we currently don't have plans or time for them, sorry.
Actually, I can see where Shroomerson's going with this one. Its more comparable to Mario Party 3's Battle Mode, where you hire partners to join you and defeat your opponent.
If this idea were altered to be more comparable to Mario Party 3's Battle Mode Partners, I can see it being a very successful and Well-Ultilized feature that would set SMBO apart from other Mario MMO's.