Well, there's a number of reasons.
Originally posted by Sheev
Anakin stomped Dooku decisively, and his power only grew from there to operation knightfall.
This is half-true. In all of Revenge of the Sith, there's only one factor that affects Anakin's ability; his fear. Fortunately, we don't have to make too many guesses about how this impacts things, as this effect is made clearly visible to the reader in the form of the metaphor of the "dead star dragon."
In the beginning of Revenge of the Sith, on the Invisible Hand, Anakin's fear is directed towards his own dark feelings, and are no doubt exacerbated by the weight of the expectations of his peers. Dooku knows this, and nearly wins the fight by exploiting this fear; however, Palpatine undermines the weight of those expectations by giving Anakin permission(an excuse) from an authority to do what he actually wanted to do--give in to, and unleash, the evil emotions that were welled up within him. In doing so, his fear subsided and he became much more powerful.
In the middle of Revenge of the Sith, alone with Palpatine, Anakin's fear comes from a different source--his own inability to save Padme, which is no doubt exacerbated by his recent suspicions of his peers. Palpatine once again plays on this, driving into him the idea that his inability was the result of the Jedi holding him back, in fear that they couldn't control him, and that by embracing the teachings of the Sith, he could obtain the power he needed, like he had against Dooku. This leads once again to Anakin quashing his fear, and irresponsibly embracing his vices, which makes him even more powerful than before.
However, at the end of Revenge of the Sith, on Mustafar in the aftermath of Operation Knightfall, Anakin's fear catches up to him. At this stage, what he fears is not what he might do or what he might lose--rather, it is what he has already done, and already lost, irrevocably. He's cut down the peers that he was striving to live up to in cold blood, and even his wife, whom he desperately wanted to save, had seemingly turned against him. And this time, Palpatine wasn't there to enable him; he was alone to wrestle with his regrets, and losing, because he was not completely Darth Vader yet.
So you see, while it's true that Anakin was at his strongest during Operation Knightfall, his wasn't a consistent power growth. It was all about his frame of mind, and alone on Mustafar, he wasn't mentally in top form.
So how in the hell did Kenobi, who was inferior to Dooku manage to contend with Anakin as well as he did, and eventually defeat him?
Well for one thing, Obi-Wan is not inferior to Dooku in all respects; he's the best at what he does, and terribly underrated on the whole. Secondly, there's the issue of compatibility. It's made clear in the novelization that, like Dooku, Obi-Wan was no match for Anakin strength-to-strength; he managed to survive as long as he did through solid defense and generously giving ground, and managed to win by luring the fight to a hazardous environment, where he could use Anakin's impulsive and erratic behavior against him.
Of course, considering the difference in strength, he might not have even managed that much were it not for their personal connection. Kenobi was Anakin's teacher, and over the course of the Clone Wars, they were said to have spent thousands of hours sparring against each other. It stands to reason that he, as someone whose fighting style revolves around prolonging combat until the opponent makes a mistake, would stand to benefit from knowing every aspect of his opponent's fighting style inside and out. After all, as strong as Anakin may or may not have become, it's not like his technique or tendencies in combat changed over the course of Revenge of the Sith. Obi-Wan had already seen everything Anakin had to offer countless times prior to their final engagement, so he was prepared to counter him, while other accomplished swordsmen (Tyranus and Drallig) were not.