I've clocked in about 1,000 hours in Phantom Pain. The game is definitely rushed and unfinished, probably one of the most polished unfinished products I've ever seen though. Firstly, the soldiers speak of things like cameras and ATV's getting brought in if you have been active in the area. There are even those missions you can send your MB teams on to counter these, but the cameras and ATV's are never implemented, at best is improved armor and weapons on the soldiers who would normally patrol. My supposition is this was meant to be even further expanded on with Helicopters and perhaps additional road patrols.
Secondly, the entire Motherbase and its systems seem like they were just the base placeholder things, as if it was never really expanded upon. Kojima talked of a much more expansive and customizable MB system, and that never appeared.
Speaking of Motherbase, the Online missions you can take involve the Skulls assaulting the base, indicating there was meant to be some further storyline involving them, as well as Quiets storyline seemingly being cut short. Not to mention other smaller storyline oddities.