I've seen many blogs about this, and I'm not quite sure if anyone has written on this subject. So, if they had, just ignore this, and have a nice day!

I'm sure Yoda is a skilled warrior in his own right, as well as Sidious. But this period in time is not the time for Jedi. For those of you who haven't read the novel of Episode III, Mathew Stover put it like this: The brighter a candle burns, the darker the shadows become.

"A Jedi can feel his strength flow from the force." - Master Yoda

"The Force is with us, master." - Count Dooku

At this point, Sidious has the force absolutely polluted with the dark side of the force. While Yoda fights Sidious, he is drawing his power from the force to guide his blade. Meanwhile, Sidious is controlling the force, meaning Yoda has no advantage over him, and he's only being manipulated. The harder Yoda fights, the more power Sidious gains. (i.e. the candle reference.) At this point, Yoda realizes he had been training Jedi for the LAST Sith battle, while the Sith had evolved. This is in part why he flees, because he knows he cannot win.

So in conclusion, the battle has nothing to do with the skills of a lightsaber, but the way the Jedi had been trained to draw energy from the force, which at that point is in the hands of Darth Sidious.