I think Machida would be faster than Shogun in a third fight, and would have a greater chance of winning. Shogun looked his best when he fought Chuck and Machida the first two times (very fast and crisp - incredibly powerful leg kicks), but since that last knee surgery (after Shogun/Machida 2) he hasn't used those kicks much at all, and seems to be a permanent step slower than he was.
However, Shogun is able to take an unusual amount of punishment and has walked through Machida's best strikes before. Machida probably won't be able to KO Shogun, but Shogun has the power to KO Machida. If they fight a third time, Shogun has a chance to land a KO strike, but it seems more likely that he would get out pointed. I'd like to see a third fight.