I thought the Naruto manga was better than the anime. The manga is a lot more faster paced without so many annoying flashbacks. There were even some episodes of the anime where the first ten minutes were dedicated to nothing but flashbacks of the previous episodes. I think the manga's art is a lot better than the anime's too. I don't like the choice of color palette Studio Pierrot uses for the anime and the eyes look much more weirder than in the manga, especially Hinata's. I personally thought her eyes looked really creepy in the anime. I don't really care so much about the music, either. And then there's the annoying and useless filler-in episodes that the anime has. I also thought the Chobits manga was better than the anime. The manga had better pacing and I thought Hideki's character was developed a lot better. The anime made Hideki too perverted and too stupid, IMO. In the manga Hideki at least knew how to turn on a computer but he didn't even know that much in the anime. The anime relies too much on fanservice (was a whole episode devoted to Chi buying a pair of panties really neccessary when the manga showed the same story in two pages?) and the ending was too rushed and cut out a lot of important plot details. I didn't like Chi's Japanese VA very much, either. She was cute when all she said was "chi" but when she spoke normally, her Japanese VA just sounded very bland and unemotional to me.
And while I actually liked the second season of the MKR anime better than the manga, I thought the first season was better in the manga. I don't like how the anime changed Ferio's role in the series. I didn't like the introduction of Inouva in the anime, either. He served no purpose in the story other than as a boring deus ex machina who's only point is to make more filler-in episodes in the anime. There are a bunch of other things I didn't like about the anime version of the first season, but they're mostly little things here and there that really bug me but are too much to list. However, I didn't like the ending to the first season at all. The anime took away all of the surprise of the plot twist by making the ending twist more obvious than the manga and the characters are just nowhere near as emotional in the anime's ending as they are in the manga. When I first finished reading the first story arc of the MKR manga, I cried at the end but I never cried at all when I finished the anime version. It just wasn't as emotionally involving as the manga. And I thought the manga's artwork was a lot more detailed and more consistent than the anime's.