I'd say it has a few more issues than that. Things like not mattering in the continuity, having a villain who doesn't have much presence in the story, characters coming out of the events of the game in much the same way as they entered.
I disagree about Skull Face not having much presence -- he has as much presence as any previous main MGS villain does, really. It just seems like it's less because now you're spending more time actually
playing than watching. You just have to go back and look at MGS3 with Volgin as an example:
You encounter Volgin for the first time during the Virtuous Mission and he has one long cutscene that starts from the bridge and then on the chopper.
Then in the Operation Snake Eater part of the game, the next time you see Volgin is after beating Ocelot/The Pain, which is also when you first see The End.
Next time after that is a scene after you've beaten The Fury and Volgin is beating up Granin in a barrel.
Then there's the time Snake gets caught in Groznyj Grad and the subsequent torture scene encounter
And finally everything from his first phase boss fight (after you've planted the C3) to an insanely long on-rails section all the way to the second phase of the Shagohod. The near-end of MGS3 is where you see Volgin
the most and comparatively I can see why you would remember Volgin more than Skull Face but the amount of times you encounter each villain is about the same -- minus Volgin clearly having slightly more screen-time than Skull Face at the end (because Volgin actually has two whole boss fights unlike Skull Face who you never even fight).
Just for the sake of it, let's go over Skull Face's appearances (including GZ because MGSV isn't just TPP, let's face it GZ was intended to be part of TPP Konami just forced Kojima to sell it as a separate product):
First encounter is during the Ground Zeroes mission where he is leaving Camp Omega.
Second encounter is Mission 6 in TPP, where you are trying to get the Honey Bee.
Third encounter is Mission 12 when Sahelanthropus is first revealed and you've rescued Huey.
Fourth encounter is Mission 20 at the Devil's House
And finally, the last encounter is mission 30/31 where he gives his big monologue like every MGS villain does before they die (even Volgin has a big monologue in MGS3 before he dies, explaining the Philosopher's Legacy and all).
So, five whole scenes (six if you want to separate 31 where he dies after you've beaten Sahelanthropus). And this isn't even including all the tapes Skull Face has in GZ and TPP, which is quite a lot.
He had about as much screen time he needed. Maybe not what you
expected (and certainly not what I expected either) or wanted (because Skull Face is a very interesting villain they could have done more with -- I certainly liked his voice, demeanor, and manner of dress) but it's on-par with previous main villains of the series for the most part. This game just has more
gameplay between those bits of villain scenes unlike the previous games, especially if you play side-ops between main missions.