For me, Clone Wars gets the edge over TFU. I like that it was mentioned in the movies, but I'm also into all the EU stuff. I don't think TFU is that much of a stretch...it has been mentioned in multiple sources that both Vader and the Emperor secretly used other force sensitive apprentices. Vader was looking for an apprentice to overthrow Palpy, and Palpy had other apprentices available should Vader need to be replaced (Hello, Mara Jade anyone?).
I think its a cool concept, as is the Vector cross-timeline story just starting up in the Dark Horse comics. But at the end of the day, the Clone Wars is just a cooler concept. An army of Jedi and and clones equipped for countless battle situations? Fighting a plethora of different droids? Local armies on both sides? Can't get much cooler than that. Unless of course, everything is release in skittles color variations.