Well, I have a few gripes with the series myself, so I may as well chip in. Though it's likely I'm repeating what others are saying:
1. The character designs. I'm not sure why they did it, but they changed pretty much every character's design a bit. Littlefoot is the most pronounced, however. You look at his face, for example, and you can see they have softened his outlines, lightened his colour scheme, rounded his face out a bit more, even chubbied up his cheeks to the point that he looks like he's perpetually smiling! And I wouldn't recognise Hyp if they didn't say that was his name, they changed him s much! Most of the other characters escaped with only minor mutilations, but still. They should have just left them as they were.
2. The songs. I have to admit, many of the songs, I enjoyed. Most of the "Big Water" rehashes and remakes, mainly because I love the original song. I think out of the ones I've heard, the only rehash of "Big Water" I don't like is the Longneck Test version, which just felt forced. A few of the other rehashed songs, and a few new songs turned out pretty good, but like the movie songs, for every good song there is at least 1 awful song.
Also, they should have just stuck to 1 song per episode. Sonic Underground did it, and they would have gotten away with it if their songs were any good. It just felt silly that they would break into song several times per episode. They can do that in feature films, but for 30-minute episodes, multiple songs just cuts out too much action.
3. Pointless fillers. There are several episodes that have absolutely nothing to teach, and contribute nothing. Why TV series have these fillers is a mystery to me.
4. Sometimes the characters were completely out of character. Sometimes this is a good thing (Like when we see Ducky's evil side), but in the cases of Doc, Ali, Mr Thicknose, and occasionally the Gang themselves, they are nothing like they used to be. Tha cheeses me off quite a bit.
Other than that, I'd say it was decent. The plots were usually relatively good, and the characters' voice actors did a decent job (Probably the better voice actor for Chomper, for example), and for the budget, many of the good songs sounded wel done (especially considering they were all done on synthesisers)