[orangemoore]

I think that it can really depend on the situation. For instance my FTC team 3507 has built a mecanum drive train this year. And as the programmer for it accounting for one side of the motors being reversed is easy in code. But it becomes very complicated to understand what the values sent to the motors should be. It that case I would have voted for reversing the wires.

A side note

If you swap the wires you shouldn't just make a mental note. You should have something visible that says they are swapped. In competition any knowledge like that will most likely be forgotten.