Geos, namely, it's extremely important to have Sun Fac hitting first to dispel debuffs (maybe someone can comment on what position he needs to be for this)...
I think @Gifafi is right on Clones...you want Fives in the last slot so that on AoE attacks, other clones will die before him. It outright breaks GAS against BSF's Wild Lightning ability.
JKR teams you theoretically want Bastilla and Yoda in the back rank so that neither of their basic attacks suck up the Foresight (Bastilla for Ability Block and Yoda for damage), though I imagine this has much less of an impact as these other teams.