It's not that hard for me to explain why I'd choose CW over TFU.
First, like Jay just said, the Clone Wars was mentioned in ANH. It fills in gaps using pieces we already knew - Obi-Wan and Anakin fighting together. Meanwhile, TFU fills in gaps using a character we've never heard of... lame. I always liked the idea of Vader personally handing the Jedi their asses and hunting them down. Using "secret apprentices" and "dark jedi" to do most of the dirty work turns Vader from bad-ass Jedi hunter to corporate Empire boss -
"Hello Secret Apprentice. What's happening? Uh… we have sort of a problem here. Yeah, you apparently didn't put one of the new coversheets on your Jedi Kill reports."

Also, the Clone Wars cartoon is filled with established main characters (Anakin, Obi-Wan, Palps, Padme, the Droids, the Clones, the Jedi, etc). Meanwhile, the TFU game only has Vader, a minor Jedi (Shaak), and a bunch of made up characters.
Add in the fact that CW will be an on-going thing with a developing storyline vs. the "one-and-done" story of TFU and it's easy for me to care more about CW than TFU.