Since you are always going to have Vaan, Vaan should always be getting levelled up. (At least I think so).
Most of the time I run two teams, the GUY team, and the GIRL team.
I tend to keep them just about even, but I have two seperate saved games right now that are different. In one, I'm building only three characters. In the other - I'M ONLY USING VAAN AS AN ACTIVE PARTY MEMBER. The "VAAN ONLY" game is to see how far I can get with only one active party member...
Whichever team you use (and call me a 'Lech', but Fran is hot looking. If I'm going to watch some characters for many hours I prefer them to be decorative) if you only use the same three party members most of the time - they are the ones that will level up.
Once you have all six party members as permanent party members - it really doesn't matter which ones you pick to be the main party.