My suggestions:
1) Better boss battles: While I did enjoy TASM as a whole, most of the boss battles were incredibly stale. Scorpion was a joke...the same battle twice. Rhino was the same old, "dodge him til he gets stuck and attack him" schtick (his second battle only had slightly more variation)...Iguana was the same as Scorpion, only you were being attacked by infected....and Vermin was barely a boss...you spent most of your time chasing him. the S-02 battle was awesome, and every battle should have been more like that one...memorable. Rhino, for example, could be rampaging through the streets, and it's your job to track him down, rescue civilians, etc etc. That's much more interesting and challenging than "web, dodge, attack".
2) A bigger city: I enjoyed having Manhattan, but I think Beenox could step it up and give us an entire New York in the next game.
3) Different (and more) petty crimes: The petty crimes/rescues, while initially fun, got very repetitive after a while. There's gotta be more than muggings, car chases, and police deadlocks going down in NYC. Have side missions where Spidey stops bank robberies in progress (like smaller versions of the black cat mission), or have Spidey track down a missing person, or has to stop a prison break....there are so many ideas that could work. Also, having to save 30 infected in one area or re-capturing the Beloit patients got incredibly tedious, especially when it's the same short mission over and over and over again. If you're going to have those missions, keep 'em to a minimum. I remember looking at my map at the number of infected I had to save, and said "f**k that" before doing something more interesting.
4) Work on the combat/upgrade system: The free flow combat system is a ton of fun, but other areas of combat need to be improved, such as web attacks. I think this is the first Spidey game where I was astounded at how little I used my webs in combat. Also, give us more of a challenge for finishing moves...I'd like to be able to execute a finisher combo on a baddie instead of just pressing one button and have Spidey do it all automatically.