Playing through diamond, I noticed that when you beat team galactic, Cyrus, unlike other evil leaders, doesn't disband his team - he just dissapears. So mayby they could do something where you are friends with Cynthia, and she is your friend when you are young, but after you beat the game, depending on your version, after the end, you can get either diagla or palkia. Diagla sends you back in time to after the events of diamond to battle cyrus, where his team reflects his team of platinum (except much stronger) because it's still in that time period. Meanwhile, in the other version, palkia sends you through space to the place where cyrus currently is, and his team, while the same levels and same general diffuculty of his past team, has more gen. 5 pokemon
Unrealated, the battle frontier should have perfect points like in battle revolution. it wouldn't be too broken if they don't carry over, and they could be usefull if you ever get haxxed by freeze or OHKOs or something