Yeah, I felt the same way about the Goblins. They had a certain impish, gangling look in Fellowship, whereas in this, they're all short and stocky, and fat in some cases.
I also got the feeling while watching this that they used a whole lot less costumed extras in this movie compared to the LotR trilogy. A shame really, considering the Uruks, orks and goblins looked frighteningly real in the trilogy.
edit- Thinking about it, I suppose it's not Jackson's fault, regarding the goblins. It's mmore Tolkeins, since he basically completely changed the goblins mannerisms between The Hobbit and LotR (made the Goblins darker than they were in the Hobbit, basically). He did the same thing with orks, changing from mostly sentient hill-billy's to generic beasts.