I actually had some pretty similar thoughts to this recently but I arrived at the same conclusions you did about its glaring shortcomings. The problem isn't that Virizion is bad, it's that it isn't the best choice for most of the roles it can fill.
It has unremarkable offensive typing for the tier - fighting is solid but isn't really complemented well by grass. It's SD sets are overshadowed by Cobalion, who can afford to run substitute instead of desperately needing Stone Edge or Gallade who can recover some HP with Drain Punch (even if it is less bulky). Non SD sets can't pick up momentum like Cobalion, don't have the threat levels of Hitmonlee, has worse coverage that Emboar (who is also a solid choice for going mixed, which Virizion really isn't), isn't as good a choice user as Medicham...
It wishes it had the support options of Ammonguss or Gourgheist.
As a special attacker, it's okay... Nobody really likes using Focus Miss as their STAB option. It lets you take hits like a monster but there are a ton of things that come in safely (most notably, frickin Tornadus but also delphox, escavalier, brokenmoth, reuniclus, yanmega, moltres, cresselia, etc).
Now, don't get me wrong: it isn't bad, per se. This just isn't the tier for it to shine.
I would have to disagree with this. Virizion is a perfect fit in RU, and most of the comparisons you made were irrelevant. You seem to say that its Grass/Fighting typing is its downfall, but its quite the opposite - that's the one thing that distinguishes Virizion from its competition. Its unique typing is its greatest asset, resisting the EdgeQuake combo and giving it important resistances to Grass, Water, and Electric - meaning it counters and sets up on completely different things than, for example, Cobalion, notably Rhyperior and Sharpedo. Think As for Grass and Fighting offensively, although it has less neutral coverage than Fighting/Steel, it has better super effective coverage. Also, Cobalion definitely cannot afford to run Substitute over Stone Edge, as that would allow many things like Moltres, Delphox, Slowking, and Jellicent to counter it. Sure, it doesn't need it nearly as badly as Virizion, but almost always runs it. Plus, it has much higher speed than Gallade, which is easily revenge killed. Of course, Cobalion and Gallade have their advantages of Virizion as well, but Virizion certainly isn't outclassed in the slightest.
Plus, Delphox, Yanmega, Moltres, Veneomoth, and Escavalier definitely cannot switch into it safely. Unless Scarfed, all of them get outsped by Virizion and OHKOed at +2 with Stone Edge (CC in the case of Escavalier if SR is up). Tornadus and other Flying-types are also a gamble, since its pretty darn easy to predict the switch-in. Plus, if you're using Virizion effectively, you'd definitely have teammates that can take care of Flying-types.
The only real set you should be running is Swords Dance, as all the other sets, including Calm Mind, are pretty much outclassed, like you said. Nobody's going to run a support set, because Amoonguss and Gourgeist do it better in most regards; nobody's going to run a All-Out Attacker or a Choiced set, because like you said, there are things that outclass it. However, it is amazing at its best set - Swords Dance, and in this role, it is defenitely not outclassed. It simply is different from the others. For example, +2 Virizion gets past many things that stop Cobalion, like Alomomola and Slowbro (even Gligar, because of Leaf Blade's higher BP), thanks to its Grass-typing. I'm not saying Virizion is better than Cobalion, but you can't say that easily that Cobalion is better than Virizion.
To conclude, Virizion is a good fit in RU; it's certainly not the best, but definitely better than your description.
Btw, Amoonguss still hard counters CM Virizion, since it usually caries Clear Smog.