Anakin lost because it was necessary to the story for him to lose.
Any in-universe explanation is only a justification for that. :P
That being said...
First off, Anakin has the high-midichlorian count of ANYONE, not just Jedi. If you're referring to the 1st highest Sith as Palpatine, I believe that's inaccurate. While we haven't had specific information about Palpatine's midichlorian count, it is reasonable to suppose that Anakin's was still higher. They remarked how he'd had the highest count ever found by the Jedi in TPM, and since he's the Chosen One, that would imply a significance to his power/potential i.e. he really DOES have the highest midichlorian count.
Also, in AotC, Palpatine tells Anakin, "I foresee you will become the greatest of all the Jedi, even more powerful than Master Yoda." In RotS, he tells Yoda, "Lord Vader will become more powerful than either of us."
Now, on to the meat of the question.
The high ground is an answer inconsistent with TPM - Maul had the high ground, yet Obi-wan was able to leap out and slice 'n' dice without being skewered himself.
The better answer is Anakin's anger and inexperience.
Remember, despite his high midichlorian count, he was said that he could/would BECOME more powerful than Yoda or Palpatine. Midichlorians are POTENTIAL, not current level of power.
However, the line between skill/experience and raw power has always been a murky one in the EU. Obviously, despite his inexperience, in AotC Anakin is noted to be extremely capable, probably due to the edge his high count gives him.