As much as I love MGSV, it's not hard to tell that it wasn't quite finished. (It's pretty apparent when
the actual last mission and resolution to several plot points isn't even in the game.)
One thing that stuck out to me is that you encounter all these ex-MSF soldiers who attack you for no explained reason while jerking around like the Skull soldiers, also for no explained reason, and then you...recruit them back into your army, and nobody ever acknowledges any part of that.