I don't know: I'm watching FC Jago's anchor Vergil vs. NerdJosh's anchor Wesker, and Wesker is making Vergil look like his bitch. SS doesn't protect Vergil's hurtbox from the top, straight or obligue angle. It also doesn't really last all that long. Not to mention Wesker can run up and command throw Vergil upon activation since it's 1 frame start up on the throw. And Jago's a pretty good player - naturally, who adopted Vergil very early on.
Anyway:
I mostly agree with everything you say. Ultimately a lot of the things required to 'protect' Vergil at least from a competitive perspective, isn't worth it since all that can be applied to other characters with quicker, and more immediately rewarding results (i.e, Wesker, Viper, Spencer, Zero, Doom, Wolverine, Magneto etc etc.)
Vergil is not S or even top A tier because of the imbalances that exist with some of the other S-tier characters. In actuality, I think Vergil is a very strongly balanced character that is only struggling because of the absurdities of some of the other top tier characters. It's hard to justify using Vergil when other characters seemingly can open up their opponents without assists or meter, and consequently build a net bar after doing a 900,000 damage combo. If Vergil uses meter to open up an opponent (spiral swords) he wastes a meter, and isn't gaining meter during the combo via spiral sword activation, and it's hard to do that much damage because of the absurd damage and hit stun scaling. At that point, just Magneto and tri-dash over your opponents head with a semi-decent assist, problem solved. Spiral Sword not required. Seth Killian really said it best day 1, "Vergil is not top tier." Maybe we see a little truth in that statement. Vergil is no Dante in terms of tournament effectiveness (thus far).