Yeah, I've played 3,4,5 player games (haven't actually played a two player game yet), and the general rules and their simplicity work perfectly for that sort of game. The activation phases suit multi player games well as there's a lot of tactical advantage to be gained if you keep your soldiers in activation range of your wiz and apprentice, even if you lose initiative.
As tyrionhalfman suggests, you'll want to turn the wiz and apprentice phases into Captain and First Mate phases, to keep the same feel.