I think Dusk actually has some pretty good ideas. Web of Shadows, if anything, proved that no matter how good the concept for a Spidey game sounds, the Spider-man 2 formula just doesn't cut it anymore.
I'd keep the free roaming in there, but like Dusk said, we're missing out on the potential to swing around the Baxter Building, hop onto the Avengers Tower, heck it'd even be awesome if there was a way you could come and go onto a S.H.I.E.L.D. hellicarrier and explore that. It's not impossible to do so, no way, its just about Activision not really caring how much effort's put into the game if they get a load of money for it.
Give us USM's heavily underrated combat, give us a plot that squeezes in a LOAD of boss fights, and give us unlockables worthy of a Spider-man game. The PS1 Spider-mans gave us a ton of great costume unlocks that actually effected the game, USM was the last to give us different costumes and even that didn't alter the game in anyway, no matter how hard you fought for the Black Suit.