Hulk had the advantage over Thor in close combat. He'd lose if he fought that way again but as they're not on the Hellicarrier here, he has no reason to fight so idiotically.
In physical strength, but not in power. He definitely had more moments but that doesn't mean it trumps the power Thor has displayed or that he'd win in a real battle.
Thor's lightning wouldn't even faze Hulk. Taking down the little alien ships was nothing impressive at all, Hawkeye did that kinda thing with his arrows.
The best feats all belonged to Hulk, from one-punching a transporter/carrier 'snake' to absolutely annihilating Loki with a casualness bordering on the ridiculous. As Hulk said, "puny god". Thor's no different.
Also, Hulk is the only Avenger to have taken direct energy attacks from dozens of alien ships. The rest had to avoid the attacks, because they couldn't/wouldn't survive them.
The Avengers was just basically Hulk's feat catalogue (volume one).
Hulk beats Thor in everything besides comics (and there it's debatable). In the movie the Hulk definitely looked better. In the Hulk VS DVD he beat Thor to within an inch of his life, and would have killed him if he didn't decide to hop away. (and that was in Thor's own home turf). In the Avengers cartoon the Hulk is the only one who could take Graviton and Thor couldn't. In fact in that cartoon, the Hulk CONSTANTLY is one-upping Thor. And in comics you have Hulk beating Thor's face in with his own hammer, Thor admitting he could never beat the Hulk, Thor getting beaten up and Hulk running away.... I think it's a safe beat the higher ups at Marvel like the Hulk more than they like Thor.
They definitely make Thor look like a chump in the Avengers cartoon. Kind of like how they make Superman look like one in the JLA cartoon. But Thor definitely gets worse treatment. I've definitely felt for a while that there's some editor at Marvel that doesn't like Thor.
I don't think Marvel are making Thor look like a chump, when it comes to films, or at least I don't think it's just limited to Thor.
Both Hulk and Thor have to be downplayed significantly, in order to give the other characters something to do and make them look like they contribute.
The Hulk has basically been reduced to comic-Thing level feats, for Hulk's own films (nothing spectacular save for the one feat of surviving a nuke in Ang Lee's Hulk), Thor's been reduced too but not as much.
It's more of how they are compared to each other. Hulk always comes out looking better in the movies/cartoons/dvds. I disagree with the comics for the most part, but there have been some writers who are really pro-Hulk. Don't believe me? Watch this: