Whenever I play a turn based RPG such as Final Fantasy, The Legend of Dragoon, Breath of Fire, Chrono Trigger etc I always have the main character in my party.
In some games that's required, but in some cases such as Chrono Trigger where you can switch Crono out of your party, I usually keep him in there anyway. It doesn't feel right otherwise. Maybe i'll switch it up every once in a while. I like to live dangerously. I'm cool with making other people leaders of the party in battle formations, as long as the main character is in it.
There are exceptions though. In Final Fantasy X I rotate anyone in the party, especially considering the enemies have specific weaknesses.
Aside from that, when an RPG has a level up system, do you let anyone have a higher level than the main character? I tend not to. It bugs me for some reason. When I play Breath of Fire, I want Ryu to be highest leveled. When I play Legend of Dragoon Dart needs to be the best.
When I play Final Fantasy VIII Squall needs to be highest leveled. It might be because I associate the main character as my conduit to the story and I want to be the best? Maybe.
Whenever I'm playing a game for the first time and I get an unsuspecting party member who is a few levels higher than me, I might shelf them until I catch up, haha.