With the potential story in mind, with perhaps more organized crime, and a continuity of first game, I can see some potential villain encounters:
1) Mr. Negative (hinted at in ASM and a gang leader)
2) Kingpin (confirmed)
3) Shocker (is a fan favourite, hasn't been used for a long time now and would fit as someone in a gang)
4) Electro (obviously)
5) Rhino (obviously)
6) Chameleon (fits the story and has been asked for alot, never been used before)
7) Green Goblin (if he shows up in the film)
8) The Spot (I've seen lots of people ask for him, and Beenox listens to fans)
9) The Enforcers (would fit the gang thing)
10) Black Cat (fits the story and had her "prequel" in the first game)
11) TSSM Tombstone (hopefully, would fit the potential story)
12) Morbius (hinted at in ASM)