Depends on the mission. If I'm off recruiting, my starter, now a Vaporeon, will be the leader, since she's level 95 and is the strongest Pokemon I have.
My partner, now a Raichu, does everything that my starter doesn't and usually ends up tagging along with her, unless I'm recruiting stuff. Then I go alone.
Training weaker Pokemon and some escort missions, Gengar (level 52) X3 Love using him by himself, since he can go through walls and everything. And he has high enough IQ to see traps. Yay!
Training baby Pokemon and long escort missions, Kingdra (level 48) I use her a lot since she mostly has long range attacks.
Lower level missions or just training, Arcanine (level 38)