Well since it has been mentioned before by Luciano that the Assassins may know of a different artifact similar to the Apple, we could pursue that? Only Elena and Alessandro wouldn't have exclusive knowledge of its existence or whereabouts, but now that they have switched sides, the Templars have a hefty list of Brotherhood allies and conspirators that could be approached and interrogated for information that they otherwise would not have had.

This could turn into some artifact of our own creation or we could tie in with the original story line and lead our characters and big bad Mr. Borgia to the papal staff, since it was the second piece of eden in Brotherhood. 

I suppose the biggest surprise at first would be the Brotherhood thinking it succeeded in its assassination of the two traitors, then watching their allies mysteriously drop like flies and be confronted with the two they thought to be rid of. Then there's Elena confronting her brother, each on opposite sides of the fight at that point. Family drama is always fun. 

Lots of little tidbits, but it's all I have at the moment. If any of it seems interesting then we can build upon it, and if not we can pursue other avenues.