Funny; those are my two favorite as well.
I think Jet Li edges out Donnie Yen, but only slightly. Yen brings a pretty good mix of martial arts to his films and they're fun to watch, but as a result, I don't think they're as cleanly choreographed as a whole, as you seem to be pointing out. His background is more eclectic, which could be positive or negative depending on your perspective. I tend to favor more of the classical methods, both in practice and in film, so that is the reason for my preferring Jet Li. Li looks better in film due to his foundation in Wushu, which is all about presentation and performance - even over martial application. He did evolve from there, though, and practices authentic Chinese martial arts and really seems to have a better understanding than most when it comes to methods in which he has trained.
To put it in perspective, though, both are so highly regarded and respected that the movie "Hero" was widely anticipated due to their fight scene together; a rematch from "Once Upon A Time in China 2". That's the main reason I went to see it too!