He's bad, but I still think he's leaps and bounds ahead of Corypheus from DA:I. I mean, you literally begin the latter by irreversibly fucking up his plan for world domination, you could not make a villain more ineffectual than that.
The problem with Skull-Face is that he had so much build-up in Ground Zeries, with all the tapes you find foreshadowing him as this weird and mysterious, fucked up dude, who nevertheless essentially shares the same goal of bringing down Cipher as Big Boss does, so when all these trailers come out that make it look like he's gonna actually team up with Diamond Dogs come out, the intrigue grew further, but then you see him in the game and he's a fucking cartoon villain, with a plan that's both retarded and essentially retreads the plot of Peace Walker, just replacing an AI with him for nuclear deterrence and with MAGIC NANOMACHINES thrown in on top. And the best part about it is that the scene where he explains his plan; the jeep ride on the way to his secret base, is probably the most poorly executed scene in the entire game. It's just so awkwardly done, with Skull-Face constantly pausing for no reason and getting uncomfortably close to Snake's face when he does talk, and Snake just sitting there silently and looking as though he's awkwardly trying to avoid eye-contact with him, it's just surreal.