Remember that Yoda basically walked into a fight with a sith (Palpatine) that he knew nothing about. While we all accept Palpatine is stronger, Yoda would have done a lot better if he'd known what he was getting into (also note that Palpatine had decades to study Yoda), and it seems clear that both Yoda and Obi-wan weren't acting that rationally in the final hours (understandable after having their friends and lives destroyed). Caedus on the other hand was a well known figure, Yoda would know exactly who he was fighting and thus would do a lot better (+ 900 years of experience far outweighs 20 odd).

I agree with a previous poster though, likely outcome would be Yoda turning Jacen back to the light.