I agree, the game is amazing!!
I don't know that I'd care about that for this game... I do know they let you restart a mission or start from your last checkpoint and I really appreciate that becuz sometimes I totally botch up a mission early or make stupid mistakes like fire a weapon when I thought I had my camera up & was zooming in on targets lol
I think I'd rather they worked on the replayability. Some of the missions would be fun to play again in context, but the main draw is the open world. So...
Allow us to skip cutscenes. Allow more customisation of the HUD and toning down of the hand holding. Do something to stop the island becoming so boring as you win the outposts. Sort out the finances so that there are still things to buy when you are loaded. Increase the difficulty. Take the randomness up a notch so that even more crazy, unpredictable stuff happens. Let me finally see and die at the hands of a Moray Eel (never seen one on PS3).
Oh, and fix the game-breaking bugs that seem to appear on a 2nd play through (that forced me to stop half way).