Don't get me wrong the game-play is absolutely fantastic and I should mainly be judging it off of that (well, since it's a game after all), but the amount of repeated/formulaic missions (go extract this guy, he's really important for whatever reason!), even in the main storyline, is far too much.
The game lacks the same tightly designed open-level structure of Ground Zeroes/Camp Omega, you rarely feel like your actually infiltrating a base from within, instead you observed and gather all the important information from the outside the borders of a base. I liked in Ground Zeroes that you were dropped off amongst the confinements of the base and forced to learn your surroundings. In the actual game, you just perch from a conveniently placed vantage point and tag everything you need. It gives you more freedom of choice on how to tackle your mission, "open infiltration", but it just disguises the lack off well thought out design. Imo the game should have just been multiple similarly sized Camp Omegas (but diverse obviously), instead of the abundant mud hut villages with a few well designed areas.
Also the whole way the story is organised is a mess. Obviously the epilogue was nicely paced and had just enough "Metal Gear-ness" without feeling too forced on the crazy side of things. Chapter 1 is technically the most complete, but even then it feels disjointed and lack structure. Nothing gets fully explained, and the supposed dark themes/taboo subject matter is rarely delved into to warrant them being there in the first place. Child soldiers? - I couldn't help but laugh when they were first introduced. The game provides more "game-y" justification of why you can't do certain things with them (hurting, fultoning, etc.) than is does explaining their story presence in the first place. They're just shoved into a cutscene for the sake of being there, followed by an escort mission of sorts where they helplessly run away as you try to keep them under control. This is just one example, and not to mention the amount of seemingly random side-op feeling missions that make up the main content. And don't get me started on Chapter 2
People should listen the the audio tapes though, Venom does talk a lot more in these and it's delivered fairly well, and it does expand on the story somewhat (even if it's all mainly "muh parasites" and other similar excuses.) I also thought that the characters felt more shallow even compared to Peace Walker, and their goals are never fulfilled. Kaz just likes to shout about revenge a lot and always seems worried whenever you fulton somebody, you don't see much of Ocelot (especially when regarding his shooting abilities except one scene), Skullface... ("SUCH A LUST FOR REVENGE, WHOOOO?"), and that car ride where Venom just sits there looking bored.
It's so blatantly obvious that the game has been chopped and changed throughout the development cycle. The amount of cut content (given how messed up Chapter 2 is, and how there was supposedly a whole other chapter left out), I'd say the game is easily missing a 1/3, or even 1/2, of the "original" content it deserves, which is such a shame. As much as I wanna hop and that Konami hating bandwagon..., KojimaPro did have a fairly sizeable budget for development alone ($80mil or so i've heard) and plenty of development time. I can't accurately comment on development seeing as I don't know much about working in Japan (especially Tokyo as i'd image it's fairly expensive wage wise for an average programmer, for example), and how much of that time n' money was spent on the Fox engine alone, but it just seems unreasonable to blame everything on Konami even given their recent actions.
Also some more specific nit picky things. The game needed more interiors, especially on Motherbase. Cassette listening system is awful given how much characters like to chime in overtime you do something. Credit sequences at the beginning of missions can potential spoiler said mission.
