What if you could pay a fee and gain a special "Synergy Power" when certain companions work together in a mission?
For example: 1. Bonnie Anne and Ratbeard could have a combined attack to do additional damage as she stuns an enemy with her gun and Ratbeard then hits the stunned foe with his peg leg. It could be called "Knock You Down a Peg" or something like that.
I think this would be fun, and would encourage the idea of using companions who have a reason to work together.