The same density of action and epicness in regards to game length They coulda easily made Rising into a 20 hour game instead of a 10ish one, but condensing the action into those few hours is what made them so worthwhile.
Present a character who fought alongside Jack during Liberian Civil War and make him an enemy. They could also create another character who lost someone precious to him by Raiden's hands during his activities as a child soldier.
Focus more on Raiden's past.
Bring back old characters.
Extend Sunny's role in the game.
I don't really think it will happen, but to see MGS Rising Back on Fox would be a real dream come true.
Honestly, they should pull a "Lost Levels" and make Metal Gear Rising 2 the original storyline for Metal Gear Solid: Rising. We know that game ended up having its story and boss concepts finalized prior to its cancellation, so it's best to put them to good use.