Tobey is a great actor people forget he's done stuff like Cider House Rules, Pleasentville and his departure from type like Wonder Boys and Seabiscuit.
Yeah he was a lot thinner in his no-shirt scene than cut in SM2 because he LOST so much weight for Seabiscuit (okay not so much compared to like Bale but quite a bit). However he gained a lot between 2 and 3 but it seems he cut it back down for 3 though (luckily).
He seems in good shape. And are you telling me Tobey never was dressed as Spider-Man during an action scene in the second or third movie? I find that hard to believe because we have pics of him in full costume on the set in the second movie like when he saves the kids at the beginning or running around on the pier and Harry's mansion and all that (well obviously Harry's mansion). Now I don't expect him to be doing the flips or CGI stuff, but I think we can safely say he was in the costume for the majority of the non-CGI shots.
Also the train scene he was unmasked the whole bit by the way.