If you have the ability to trade, there's a very easy way to get all 3 starters.
1) Start up both games, pick different starters on both.
2) Pick one game to recieve a starter. I'll call this one the storage game (since it will store up to 6 starters!)
3) Trade over the starter from the other cart, so the storage game has 2 starters on it.
4) Reset the other cart, and start a new game
5) Keep getting a different starter each time, until you have 2 of each starter on the storage game.
6) Now, trade back 3 of the starters from the storage game to the other cart, making sure they have different ID numbers (this gives them all 1.5 times Exp bonus, letting them level easier) to the cart.