You want to know my two biggest gripes with this game. The first, and biggest, is the lack of any sense or understanding to why certain missions unlock and when they will unlock. This especially becomes a problem in the last 25% of the game.
The second, was the random times it takes to get from one place to another. The whole helicopter sequence takes way too long. From calling it in to a landing zone to just starting the mission. I REALLY wish I had known about the cardboard box shipping thing earlier than the last 5% of my game. Shipping yourself to different areas on Mother Base and to the fast travel spots you have found the shipping invoices for in the game, literally takes about 15 seconds. If you try to return to the ACC and then go to a new spot on the map it takes 2 minutes or more. It just makes no sense.