Let's see....in no particular order:
Tsubasa Reservoir Chronicle:
-Left an open ending, as though the series is unfinished. Like, three episodes at most away from how it actually ended.
-Strayed rather far from the manga for some parts.
Chobits:
-Ending not quite like the manga. (But only until the last minute or so, when suddenly it becomes the correct ending. I was almost very very mad.)
-Strayed from the manga at some parts.
Umineko no Naku Koro Ni:
-COMPLETELY OPEN FREAKING ENDING! The anime ended in 2009! Is there a season two? NOT YET!! Will there be a season two? THERE BETTER BE!!
-The gore was censored! (although, whilst reading the manga, that might be a GOOD thing...)
Higurashi no Naku Koro Ni:
-It...it's still not over yet. Even though the ending was wrapped up quite QUITE nicely, they have a fourth season/second OVA series! D: why can't they just live in peace already?
-Never really find out if Satoshi is okay or not.
-Never find out if there is a cure for Hinamizawa Syndrome.
-The English voice for Rena is freaking IRRITATING. (Female English voice actors for the girly characters is often a major turnoff for me.)
-Didn't have an anime form of the Demon Exposing Arc! That's one of my favorite manga arcs...
Clannad:
-Too sad.
-Too sad.
-Too sad!
-And yet, it's funny as well. I was laughing with tears in my eyes at one point.
-Of course, this and the above aren't reasons why it may be disliked. Clannad is.... I mean, the reason it's my favorite anime is exactly BECAUSE I was laughing right after crying at one part. It really gets in touch with your emotions and really leaves you thinking, you know?
CardCaptor Sakura (US: Cardcaptors)
-English dub was done by 4Kids! (Automatically means it sucks pretty badly compared to the Japanese dub)
-WAY too many cards. Compared to the original 19 or so cards in the manga, the anime has 40-something! Stick to the manga people!
-Strayed from the manga quite a lot, but only because there were so many cards.
-The English dub only aired to a few episodes into the third season, I think (either that or about halfway through the second.) Every episode and both movies were dubbed, just not released.
Angel Beats!:
-Totally lighthearted and funny....until you reach episode 10. Then it gets to be a real tear jerker.
xxxHolic:
-I...I'm gonna come right out and admit I've only seen the first episode and the movie (but I've read most of the manga, and it's one of my favorites)...but....but this anime is really freaking...trippy....like, Watanuki's movements are...really...ah...exagerated? and....really really...weird....yet....I love the anime!
Shikabane Hime (Corpse Princess):
-It doesn't really follow the manga as well as it could.
Pokemon:
-...Come on. Let's all be mature here and admit that, after they got rid of Misty and went to Hoenn, the anime started...lacking.
-Ash is STILL ten.
-Pikachu lost to a level 5-10 Snivy!! When it should be, like, level 9000!
-Ash is still the main character.
-Team Rocket got old.
-Brock stuck around way too long.
(Although I will admit that I still love every episode up until they left Johto.)
Hetalia: Axis Powers:
-....wait, no. I'll be totally honest and say I find nothing wrong with this anime.
-Oh, wait. America is irritating.
I feel really really mature that I was able to admit all that. :D
