Now to start It's important to note that Japanese copyright laws are very very different than many are use to. Rights that a creator has over their manga series are not nearly as protected if their intellectual properties cross over into a different medium. That is to say unless a creator shells out an insane amount of money, an anime studio can lease the rights to a series, butcher it utterly - and the writer can do little about it.
A great example of this is the series Dessert punk. Perhaps not the biggest “ in your face” series, but has a decent following none the less. Most people in North America really only know the anime series. While having its moments is overly comical and filled with more big boob and urine gags than a collage fraternity house. That's not to say the Manga was lacking them, however the anime studios took that side and ran with it, over played them and wrote in a huge swath of new ones to the point that any of the serious aspects of the series were lost in an otaku nerdgasm. In contrast the Manga took a much darker route and had some powerful moments. It's not the only example out there, but one that came most to mind. I'm sure anyone out there can site countless examples of this.