Well, by switching their costumes, you switch who is lead. 1st, 3rd, 5th costumes Popo leads, 2nd, 4th, whatever, Nana leads. So both get to lead in Brawl.
BUT I do think that having either character able to become lead after one dies could be a very nice, reasonable change. It's not really hard to switch from one to the other once one of them dies (ie: when Popo is flying off into the distance after being launched, I often try to throw out a quick fsmash with Nana--though it hardly ever works out). I think that's the most reasonable, very possible change to be made proposed in this thread.
What'd also be nice is to have Belay (B+Up) cancel-able so that you can use it purely for desync.
So, say I belay: Nana is teleported to Popo, nana thrown up and slightly forward first, and if you choose to cancel, Nana will pull Popo up, and Popo will be the first to be able to attack, and after a short delay, which will make the effort worth it, Nana will be able to attack. The delay will be optimal, so that Nana's identical attacks are spaced out from Popo's.
Depending on when you cancel, it might be similar to a shorthop or a full regular jump.