I consider MGSV to be my GOTY already, but the inclusion of Mission 51 would've definitely helped a bit with fixing the story. Chapter 3 "Peace" as a whole I believe it to initiate when Nuclear Disarmament is completed.
I'm disappointed that Chapter 2 missions were largely just reused, which is just a shame. Not to say I didn't like the Total Stealth and Subsistence missions weren't cool, but the world is so large we've could have had so much more variety. That's what bums me out the most about the game, in reality.
I mean a camera was shown off in the MGO3 announcement trailer, and if that was kept in game we could have had so much more variety in missions. Getting recon of a transported prisoner/weapon/commander/animal, taking evidence of an assassination, etc. The Ghost Photography and Secret Photo ops in Peace Walker were a lot of fun, definitely could have seen that in MGSV.
Back on topic, Mission 51 has an amazing premise and execution, and a real shame that Konami had to rush the game out when KJPro wasn't done.