I'm not sure how to put this, since I don't want to be super-spoilery, but I think the Peter/Gwen thing is all about Peter Parker being missing. I think that the Peter Parker we have right now is actually "Jessica Drew", the female clone of Peter, who has all his memories and his distinct personality. This means several things,
1. Major shake-ups for the Ultimate universe, ala Ultimatum 2. A genuine Peter Parker in the role of Spider-Man, but not the Peter Parker we're used to 3. A way to spread out Spider-"Person"'s appeal to both genders
Not to mention the actual size of Spider-Man, in the same sort of way that Peter Pan is always played by a woman...