I have no idea why someone feels the need to reboot the Spider-Man series, as Spider-Man and Spider-Man 2 were both very good, and to re-do the series without Sam Raimi directing seems like a mistake to me.
However, if they insist on a do-over, here are some villain ideas they didn't get around to in the first three movies:
- Scorpion: always a cool villain and threat to Spider-Man, plus J. Jonah Jameson is partially responsible for his creation, so there's a subplot waiting to be used.
- Mysterio: probably my favorite weird Spider-Man villain, and his use of illusions to trick Spidey and commit crimes would be a cool use of CGI
- Rhino: another good mid-level villain, and a fight between the two would also probably lead to some cool CGI effects, like Spider-Man using webs to slingshot a rock back at Rhino after Rhino throws it
Also, The Vulture, Shocker, Kraven the Hunter, the Spider-Slayer robots(also masterminded by JJJ), and even obscure ones like Hydro-Man, Hammerhead, Molten Man or The Chameleon could be used, even if it's just in a montage.