I agree with all the above, and would add that Shogun finished the fight without a mark on him (and barely breathing heavily) while Machida's legs were a mess, his floating rib (where Shogun's jump round kick landed) looked very unhealthy and the claret was flowing down his mug. Machida got one offensive flurry in - in the 3rd - and that was it as far as I could see.
Ridiculous decision which the crowd - and even the ring commentator - acknowledged.
I should add that Machida's long stance leaves him wide open to low kicks, though it was the knees in the clinch that hurt him. I admit I have never seen him fight before, but in this case I was severely unimpressed: What does he have? Untactical stance, weak kicks (a karate footsweep vs a Thai low kick? No contest) no significant boxing ability, and no apparent groundwork. Yes, he was elusive, yes he took some heavy shots and yes he had fair reactions, but champions need more than this. Ali was not the heaviest hitter, but at least he was entertaining.