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!
Sideous though probably had significantly more knowledge of Sith tricks than Caedus though, Luke Skywalker actually would have killed Caedus in the book Inferno
, he only stopped because of something that Ben Skywalker said, and Luke knew that if he killed Caedus then, he'd lose his son to the darkside.
Then in Invincible
, Luke refused to go after Caedus because Luke was afraid he wanted it too much, he was afraid he'd go over to the darkside (yes Caedus would die in the process), and become something even worse than Caedus.
Darth Caedus nearly got killed by Mara Jade Skywalker, he only barely won, he got the stuffing beat out of him by Luke Skywalker, and would have been killed if not for Ben being in danger of falling to the darkside. Hell, Caedus nearly ended up getting impaled by Ben, and only reason he didn't was Lowbacca's bad timing.
Even if Caedus was stronger in the force than Sideous, he also pulled a lot of stupid stunts that if not for other people's idiocy or bad timing, or someone's kid being emotionally unstable, would have gotten him killed many times over his brief reign. I think Yoda would have won, regardless of whether or not Caedus was stronger in the force, because Caedus made more stupid mistakes in his brief reign than Sideous did over his entire lifetime.