As much as I enjoyed Chowder, I'll admit the later episodes were pretty hit-and-miss. I think some of the best episodes came from late season one, but that's just me.
One thing I disliked about the show was that it had a lot of "dead horse gags", jokes that were repeated over and over each episode until they just stopped being funny. The "break the fourth wall" jokes were funny until they decided to put like three of them into every episode. Same goes for the visual puns. It got to the point that even the characters themselves thought they were stupid. And even THAT got tired after a while.
Gazpacho also started to get on my nerves as well. He's a funny character, but I just got tired of seeing him in every episode. At one point I swear they were just writing him in for no reason.
My favorite characters to come out of Chowder were Gorgonzola and Ceviche. Unfortunately they missed just about every opportunity to develop their characters further. The most character development he got was in "The Apprentice Games" where it's implied that his master emotionally abuses him. It's one of my favorite episodes for that reason, because up until that point I just thought of him as the stereotypical cartoon bully when in reality he was much more than that. This was also elaborated on (somewhat) in the Christmas special, another one of my favorites. Chowder makes him a sweater and Gorgonzola is so happy he breaks down in tears and runs away bawling. Awwwww.
In one episode, Ceviche was shown as the "nice kid" who donated canned goods and walked old ladies across the street. This was never elaborated on and he spent the rest of his time on the series crushing over Panini.
There were plenty of throwaway characters too, like Marmalade, who I was almost certain was going to become a regular cast member. And Stilton, Gorgonzola's mentor, who only had one speaking role during the entire show.
As for Chowder himself, he got pretty annoying as the series went on, but not enough to stop me from watching the show altogether. To me, he was still the same character on the inside. He just liked SCREAMING A LOT now.
I could go on and on about the negative aspects of the show, but I won't because out of all the missed opportunities, horrible puns and fart jokes, the show is still enjoyable.