Shogun's conditioning is always suspect and he is not consistent enough "yet" to get the accolades that Anderson does. Shogun at his best is remarkable, but his best doesn't always show up, he is suspect and when he has a less than impressive performance it results in him losing.
You seem like a fairly knowledgeable and articulate guy - which is why I'm so surprised that you're making these fleeting comments about Shogun's conditioning. It's well-known that he underwent two reconstructive knee-surgeries prior to his matches against Griffin and Coleman. Naturally, his conditioning would be shot after that. But considering his fight history, his conditioning is excellent. Both looking back at his days in Pride, and to the fights he's had since Coleman - he is very much back.
It's easy to discredit Machida in retrospect - it's always easy to claim that a fighter was overrated once he's lost (I'm not taking stabs at you), but the truth is that Machida was undefeated, and had a perplexing game that no-one was able to crack. He was hard to hit, an effective countertriker, and he had an uncanny takedown defense. Say what you will, that's a very complete skillset to rely on.
Anderson's reputation now is what Machida's was a year ago. He just hasn't had the proper opposition to test him prior to Chael. You could argue Silva's greatness when he took a beating for four and a half rounds, only to nick a sub in the final minutes - but that would be disregarding Chael's notoriously poor submission defense.
While remarkable, the triangle choke wasn't the huge surprise of the fight - but rather that Chael showed that it's possible to crack Anderson Silva once you put him under pressure. Furthermore - the fact that he actually started schooling Silva at his own game on the feet only served to further chip away at Anderson's image.
While he possesses quite an impressive talent, I can't quite say that Anderson or his team are known to be particularly cerebral - Anderson has out-shined his opposition, not out-thought it. He didn't beat Maia, Griffin and Sonnen by exploiting holes in their game - he beat them by imposing his own.
Contrast that starkly to what Shogun and his team accomplished against Machida. It's even more uncanny when training footage showed that Shogun was drilling the exact counter that put Machida out, weeks prior to the fight. Their first fight was already a strategical masterpiece - but the second set the fact in stone: Shogun has got the best gameplanning team of the sport. If he so thoroughly defeated a man who had one of the most solid reputations of the organization - can you imagine what he'd come up with for Silva?
