Manga. Without a doubt.
Which is a major shame, because the anime has the potential to be amazing. But, like Emiko said, they're just skimming the surface of the storyline. The VAs and music are amazing - Daisuke Namikawa is exactly how I imagined Fai to sound, and it sounds to me like they put a lot of effort into the voices. But the artwork seems sloppy and awkward - as has been mentioned, the style doesn't translate very well into moving form from the original manga.
Another thing is also the fillers and relationships. The only fillers I found worth watching were episode 16 (which just made me laugh like a drain...'Hyu~!' 'GET BACK HERE!!!') and the Mokona doodle episode because...well...Bee Train were obviously smoking something very good for that episode.
But what annoys me the most is how Bee Train have completely disregarded Kurogane and Fai's relationship. I know I am a KuroFai fangirl, but I can see it from a non-bias POV, and even if I didn't like that pairing I'd still be drawn to their unique relationship, and character qualities. The anime has made them into pure comic relief, which they were in the manga, but there weren't only the comic relief. The focus in the anime is almost completely on Syaoran and Sakura who, don't get me wrong I do love them, are so boring compared to Kurogane and Fai. Even their relationship seems monotonous compared to Kurogane and Fai's. But Bee Train have taken away their relationship - be it seen in a romantic sense, or purely friendship (...*does prefer the former* XD) - in order to focus on Syaoran and Sakura's 'cutesy' relationship.
Tsubasa isn't really a kids manga. So why are they turning it into a kids anime? I mean, one of the funniest scenes in all of Tsubasa in my opinion is when Syaoran, Sakura, Mokona and Fai all get drunk in Outo. And that got taken out of the anime. I will confess though, the first season wasn't so bad. I quite enjoyed it. But the second season is so rushed, like Bee Train feel they should be catching up with Clamp...or maybe that 'if they rush it they can put in more fillers.
Which brings me on to my final point. I hate the fact they did a FaiXChi episode. I say this so many times it should be my catchphrase: Does nobody remember Hideki?! Hideki, not Fai, is and will always be Chi's canon pairing. And, as Rekall said, Chi is a constructed life form. That's probably why she hasn't been seen in other worlds yet. She was a constructed life form in Chobits, and in Tsubasa. So going and making her human is...well...raping the canon. Badly. I wish Bee Train would stop assuming and pushing for other relationships, ignoring the fact that Chi hasn't shown up since the beginning of Tsubasa and Tomoyo seemed far more taken with Sakura in Piffle.
...Sorry if that's pretty long. But you may've guessed I'm not an anime fan by now. Ohoho...