Well, this being a series I hold very dear, this is a kinda hard topic for me, but I do have a few major qualms:
1. "Imaginary Friend". It's probably the closest thing the series has gotten to having a Big Lipped Alligator Moment (A sequence in a film that has nothing to do with the plot, comes out of nowhere, is totally over the top, and is never mentioned again after it ends). The segue into the song wasn't too bad, but as soon as I saw Petrie drumming on the shells of those turtles, I knew this song was gonna blow. It just seemed a little too bizarre for them, the designs of the imaginary friends didn't really look like creatures that dinosars could devise, and dinosaurs really should never sing reggae. Plus, how as soon as the song was over, the message was pretty much void (since Mo appeared a proved that he wasn't imaginary).
Most of the other songs, I can stand to listen to. In fact with several, I really enjoy them. I know they lighten the mood of the films, but I realy don't care. I've just learned to accept that they weren't made by Don Bluth, and I've moved on with it.
The only other songs I have a really hard time sitting through are "One of Us Now" and "Friends For Dinner". The former, because it just seems kinda out of place and just doesn't sound that good, and the latter because Chomper's voice actor can barely act, let alone sing!
(Note, this is not including the TV series songs, which are an entire different matter)
2. The Yellow Bellies. These characters had some potential. Their personalities and actions were pretty funny, and the way they thought and did things on a whim, kinda reminded me of me. The only major problem I had with them was their design. It looks more akin to an alien from a Hanna-Barbera cartoon than a dinosaur. The Flintstones could have gotten away with it, but LBT has always maintained a certain degree of accuracy with their designs, so they just seemed comletely out of place. Those gigantic bellies and posteriers that make one wonder how they can stand up straight, and that whole belly-bouncing thing made me cringe. If they could have just kept a little closer to the design of the dinosaur they are based on, it could have worked.
Incidentally, one reason I think that the final film was so different was because it had a different director to the other sequels, for some reason.