WARNING: This is my personal opinion of how the Amazing Spider-man 2 story should be made! Do not read if you are narrow-minded.
Also Spoiler Alert!!
The Amazing Spider-man left off on a good note... until you see the after-credit scene. At the end of the movie, Peter promises Cpt. Stacy that he would cut things off with poor Gwen... as all the Spidey fans know, he lied. And that will lead us into the new story.
In the comics, Gwen is killed off by the infamous Green Goblin. She is thrown off of a bridge, only to be caught by Spidey's webbing... little did he realize, he kinda sorta broke her neck in the meantime. For all of you who have not seen the original Spider-Man movie, the Green Goblin throws Mary Jane Watson off of a bridge and Spider-Man saves her... no broken neck, everything is just dandy. Most likely, this event will not take place again, even if it is a different girl.
In my personal opinion, I think it would create a deeper impact if they continue Peter and Gwen's relationship in the second movie, and THEN kill her in the third. Now there's a dramatic conclusion. Shakespeare style.
As for the mysterious person in Curt Conner's cell, I would like to see Norman Osbourn (even though the writers deny it being him), or Electro.
The setting could be placed near Peter's high school graduation, and he is in a more stable being.
Let me know your thoughts!!