Re: What's the diff?
2 wire simply swaps power and ground wires to reverse direction (hooks up power to wire A and ground to wire B for up, Power to wire B and ground to wire A for down). 3 wire has 2 different windings with a common ground, you apply power to one winding for up, apply it to the other winding for down, ground always stays connected to the same place. If your boat/motor is already wired for one, you would have to modify/adapt the wiring to support the other. It's not terribly difficult.
Others here can tell you about any mechanical or performance differences, if they exist.