The Jedi numbers were severely depleted by that stage.
Remember the sith "rule of two" means that all the dark side midi-chlorians are only shared out by only a couple of force users. Conversely the balancing number of light side midi-chlorians have to be shared out among many, many Jedi.
By the end of the film though, there are hardly any Jedi left and therefore Obi-Wan can call upon a lot more midi-chlorians than at the start. In fact there are only two of them left and we see Palpatine and Yoda (the other Jedi) battle out an almost even draw.
Therefore, scientifically speaking, it stands to reason that they should have been more or less evenly matched...