I love Yoda, and that is why I'm sitting here making excuses for him. Well, maybe they're not excuses...

Theory I~ As Yoda taught Luke on Dagobah, the Force binds the universe together, and for Yoda, the Jedi were what binded him together. In the Great Jedi Purge, all of the Jedi were massacred during the execution of Order 66. Perhaps that when Yoda was dueling Sidious, the Jedi were not all there to bind the Light Side (Or the Ashla; Whatever you want to call it.) together, making it weaker. With the Force weaker now, Yoda could not access or use the Force as easily, making him weaker and more vulnerable. Perhaps if all of the Jedi were there, Yoda could have been victorious.

Theory II~ This one isn't quite a theory, because I read it on http://wookieepedia.com, which is always a valuable and reliable source. The site stated that Yoda got a slight but clouded glimpse of the future, telling him that he still had an important role in the Galaxy, and that he could still help defeat evil. I believe that this vision was referring to his part in the training of Luke Skywalker. He could not risk dying, because he felt weak from fighting so hard, and falling several hundered feet, so he deserted the battle, and escaped with Bail Organa.

Theory III~ I also read in some official Star Wars source, (I Forget What) that Yoda's spirits were broken from all of the Jedi deaths. This sort of ties in with theory I. If you consider this, how would you react if you had to fight a Sith Lord after almost everyone that you cared for was dead? Well, yes, you would probably run around in a crazy bloodlust, but Jedi aren't supposed to do this.

Feel free to comment. I appreciate your feedback.
May the Force be with you!
God Bless!