What we do in my group is 'blind' list building.
We draw schemes and strats. Then each player make 2 lists, both 25ss, one lead by a master and the other by an henchman. Only after you roll for the teams and each team choose which of its player will play the master and the henchman. For example we roll teams to be A-C and B-D. Then A will play his master list and C his henchman one, or A play his henchman and C his master.
This way you avoid too silly combos.
The other way around is too make it very clear to everyone that you can do any mix so the goal is to find the most broken synergies.