I frankly couldn't care less about "Star Wars canon" these days... it seems more a marketing gimmick to appease certain fans (who care about such things) than anything. Originally it was supposed to keep Expanded Universe writers on track with keeping their stories straight with each other. That was before the Prequels, which basically ignored most of what came before.
These days pretty much "everything" is canon at some level.
So video game storylines routinely are made to be "C-canon." Obviously the player choices in-game don't count, only the overall story and characters (and if multiple endings, they pick one).
Frankly, I don't feel like TFU gels very well with the movies, but I really don't care. If the game is well put together and fun, I don't care if it has Luke Skywalker as a bad guy or Yoda as a wookiee. A solid (in-game) storyline is nice, and being true to the "spirit" of the movies is a selling point, but I am not really interested one way or the other if it goes along with previously established continuity.
That said, if they're going to make a sequel, I do expect it to follow the previous game (there's that "in-universe continuity" thing), unless it's an alternate storyline (sort of like what the DLC was for the first game).
Still, I know "canon" matters to a lot of Star Wars fans. My advice is don't take it too seriously. There are all sorts of problems across the Star Wars franchise, and George Lucas, seems least of all concerned about making sure the story flows together and the characters are consistent. If he makes that live action TV series, I predict it will just get worse.
For me, I realize the whole thing is fictional entertainment created for profit. So I can suspend disbelief and enjoy whatever is in front of me for what it is. Ultimately for me "Star Wars" is about the movies, and the first three were the best. If something sucks, I shrug and ignore it. It's not worth my time anymore to try to rationalize all the inconsistencies. Games are a different matter... to me the gameplay matters far more than the story (or the graphics). Star Wars is just a hook. Sure, if you're going to make it Star Wars, a little consistency is nice, but not the end-all, be-all.
Anyway, that's another rant for another day...
So yeah, TFU and TFU2 are just as "canon" as any other Star Wars video game. Pretty much everything licensed is "canon" these days at some level (don't know where "Darth Tater" and the Star Wars transformers or the super deformed series for babies fit though, but I'm sure somebody is hard at work on it, lol).
PS: Wookieepedia isn't canon. But you knew that already.