I completely agree with you, Kuromori ^^ Sometimes, as a devoted fan of the manga, I almost want to cry when I watch the anime (and I even sub it for my spanish fansub group, so I'm kind of "forced" to watch every episode three of four times, sometimes even more... and that's like seeing every bad character design/animation/whatever through a magnifying glass). But after all, an animated series is a completely different media, so it's obvious that it won't be a exact copy of the manga we all love.
And I don't like to blame BeeTrain for, basically, changing the target audience of the series (because most of the changes we're seeing it's because of that: not understanding that Tsubasa is not aimed at the same public than, say, Card Captor Sakura). BeeTrain made great animes of excellent quality in the past that I truly enjoyed watching, with deeply complex and philosophical stories with profound metaphors and sometimes with mature themes and scenes (not a lot of those, but anyway... ^^u) such as .hack//SIGN, .hack//Roots, Noir, Avenger, Arc The Lad...
I think the one to blame is NHK, which also broadcasted Card Captor Sakura (and if I'm not mistaken, they started doing it again when Tsubasa started being aired) and whom, I think, bought Tsubasa as a kind of "CCS 2nd Part", then making that error on the target audience. Of course, BeeTrain has its share of fault, because the low quality of the animation in some episodes has nothing to do with NHK. But the lack of blood and homosexual relationships, those pointless fillers in which sometimes they mess up the original story, the modification of Sakura's personality transforming her into a typical and boring "damsel in distress", and sometimes forcing SakuraxSyaoran moments that aren't in the manga (I shouldn't complain about that, since I'm a SxS fan too, but... ^^u)... had led me to believe that they want to sell this as a marketing product, a CCS revival, a low quality anime that, no matter how cheap it is, will help them sell a lot of merchandise. And they're indicating BeeTrain that this is what they want, so this is what they should make and produce for them.
Despite all that, if I were a member of CLAMP, I wouldn't have chosen BeeTrain for Tsubasa. Much as I like them, Tsubasa's story it's not their style AT ALL. I would have chosen MADHOUSE or even Pierrot instead.
Finally, I don't know if everybody knows this (sorry if you do already ^^u), but BeeTrain is a subsidiary of Production I.G. While IG usually does movies, OVAs and short animations, such as openings and endings for videogames (they've done quite a few series too, but usually they only collaborate partially, they're fully in charge of everything only when there's a lot of money involved XD), BeeTrain is usually in charge of cheaper *cough* TV series.