I think one of the better reasons to split up was given in VIII when Selphie decides she has to try and rescue Balamb knowing she'd failed Trabia. They actually handled that quite well, though it became a massive popularity contest on characters since you essentially had to choose between Zell and Rinoa for most of the first half of Disc 2. I also like how the inclusion of Rinoa in the Missile Base team sparked a few lines of interaction which helped beef up the love story between her and Squall even if she wasn't there for the actual romance plot. Something which could've been horrendously overlooked. As I said in my thread in the FFVIII section, I'd have loved a bit more content in this part of the game, I'd have also have loved a lot more action with the space/esthar plot arc. I think that Square missed a major "mini" game feature here where in Esthar you could have chosen to have side missions involving cleansing Esthar of the Lunar Cry's affects. I know they essentially say "there'll be a lot of work for SeeD and Garden with this in future" but it'd have been cool to have stuff like quests where Squall wouldn't necessarily be a part of it or even dispatch missions where you can't use 3 members for a while.

One of the best instances of managing player characters was probably X, Before you begin to master every job as every character the game provides you with several options to field, do you go for Wakka's accuracy? Tidus' Speed? Do you Summon with Yuna? Do you bring Auron to bear with his destructive power? However they never once took those options away from you except for plot pieces the entire party travelled at once, together (though it'd have been nice to maybe have more than just Tidus shown on screen but the party was kinda big I guess) and you could change the battle line up whenever you wished. Of course this made levelling up a little easy if tiresome since all you had to do was switch everyone in for at least 1 round where they had to do nothing but guard/defend.