I really want to like anime, because I have friends who are into it, but I just can't get into it. (Same deal wit Harry Potter, but for different reasons)
The pacing is almost universally awful. You can't take 8-20 pages of a comic (and yes, manga are comics, don't be silly) and turn it into 22 minutes of animation (15 after subtracting for overly long intro, overly long recap, and overly long teaser for the next episode) especially when it's action oriented. An entire episode can go by with nothing happening. Hell, sometimes four or five episodes with no real progress. As in, you could skip those episodes and not really miss anything. It feels like it could have been two or three minutes long, but it takes 30 minutes of my life I can't get back.
The overly serialised nature gets to me too. It's a symptom of the previous problem but it annoys me in entertainment in general. In a medical or police drama, they have a case they get through by the end of the episode, but at the same time the relationships between the characters are explored, and the overarcing plot advances itself. With anime, so often it's all the long term narrative, and often it doesn't really move forward at all.
When none of the main characters ever die, or don't stay dead. It makes everything feel like it doesn't matter who wins or loses. Who cares what kind of dangerous situations the cast get into when you know everyone is going to be fine?
Size and muscle mass having no bearing on strength. I get that it started as a subversion of expectations. But at this point it feels more like the rule than the exception. Especially children beating up muscly adults. If they explain it away as the little guy is magic or a robot, I guess it's okay, but most of the time it's just stupid.
Timing the English dub to match the Japanese speech patterns. They could do it like video games where it doesn't match and we don't care. Or they could do it like DBZA where they reanimate some parts for better lip sync. But no, they do it the dumbest way possible. Japanese and English speech patterns are radically different; when you translate it like this, it just sounds weird and stilted.
When all the female characters have the same face, and can only be differentiated by hairstyles, clothing, and breast size.
Male characters who look like female characters, and sound like females too. It wouldn't bug me so much if it didn't come up so often.
There's probably more. But that's all I an come up with for now.