One of the biggest problems is the comic panel style that the movie shoves in your face. It adds nothing and only draws attention to itself, pulling you out of the experience. Something cool will be happening and then some panel thing pops up getting in the way. Ang Lee has a great eye for visuals, so this was just a baffling decision.
The backstory with Banner's dad experimenting on himself which then passed over to his son who then gets into gamma ray accident. You could've omitted that whole thing and just skipped to the gamma rays, there's was no need for some long, overly complicated explaination. What matters is that he becomes the Hulk.
Nearly every scene where characters are interacting with one another is painfully awkward. There's also no on-screen chemistry between Eric Bana and Jennifer Connelly. And a lot if not all scenes that are supposed to be serious and dramatic come across as comical. Remember the scene right after Banner's accident where he's spasming in the hospital bed, but it looks so much like he's angrily jerking off? Yeah, stuff like that.
The rest of the issues are tied to the character of the Hulk and are not necessarily the movie's fault, like the lack of a good villain, and the Hulk just not being an interesting enough character to carry a whole movie.
I had no problem with the CGI quality or even the Hulk looking as green as he did. It was mainly the weird puffy boy face he was sporting.
I definitly prefer it over The Incredible Hulk, but then that movie was total garbage. Ang Lee's Hulk at least has some artistic merrit to it. I also liked the Hulk transformations and how he moved. And that first transformation where he's in the lab and just smashing through shit is great.
Overall though, the movie is just an awkward mess.