Thought I posted here already but maybe I got logged out:

Neither of them is small-time. Yoda has years of experience, but Jacen had been fighting in wars since he was a kid, and against enemies with a unique strength against force-sensitives that even Sith don't possess.
Both have tricks up their sleeves, but Caedus may have the edge here given just how many rare techniques he came across in his journies.
Even if Yoda is stronger in the Force, I think we can all agree that, Force-enhancement aside, Caedus is physically far stronger than Yoda, and that does count for something.
As was said, Luke is the most powerful Jedi by that era, and Caedus held his own (though granted it didn't exactly go well) against Luke for a while.

Overall, then, I'd give the edge to Caedus, except for one thing----Caedus will soon be retconned out of existence, while Yoda never will be. So I guess Yoda wins by default!