Looking at that list you put together, 5 out of the first 7 Pokemon you listed can OHKO Crobat after rocks if they anticipate the switch and use the appropriate move. That's not exactly what I'd call "being able to switch in with little trouble". Out of your list of walls/tanks, Crobat will have to risk being burned by Swampert, Suicune, Milotic, Blastoise, and Dusclops if it switches in. If Suicune uses Calm Mind as you switch in, you lose whether it's Offensive or Resttalk. If Togekiss uses Thunder Wave or Nasty Plot, you lose. Whether you beat them 1 on 1 is irrelevant because that situation is rarely going to present itself. Even if it does, you're not going to come out on top every time; there are too many variables that could change the outcome like Scald burns, non-standard movesets, etc. I can tell you right now you will flat out lose against Swampert and offensive Suicune. Crobat is a shaky check to pretty much every metagame relevant Pokemon you listed in that post, so I don't see how you can argue that it's S-tier material.I completely disagree with a few of these last changes.
For one, Crobat is definitely S-tier material; refer to this post for my reasoning. Cofagrigus, while great, is not S-tier material. Why? It's one of those Pokemon that performs excellently against the average ladder player, but not nearly as well against one of a higher caliber (it's not easy doing a two-turn setup). In fact, I don't even think it's A-tier material--high B-tier definitely; A-tier is kinda questionable imo, but I don't feel too strongly about it.
(Why did you move it down anyway? No one's even debated it being S-tier)
Weavile and Porygon2 should stay in B and Zapdos should move down to A.
As for the whole Nidoqueen vs Nidoking debacle: neither one is A-tier worthy imo. Nidoqueen is high B-tier and Nidoking is low B-tier.
I did say that its most effective sets are offensive, which means I don't think its defensive sets are effective. I'm skeptical of any defensive Pokemon that bears a weakness to Stealth Rock. In Zapdos's case, if Stealth Rock is on the field Flygon's Outrage, Heracross's Stone Edge, and Ambipom's Return are all 2HKO's, and Zapdos is slower in each case. If it requires a Spinner to perform decently, then it's not S-tier material in my opinion. I'll give you Sub Roost Zapdos though, I overlooked it and it is one of Zapdos's best sets.Heck I'll debate that. I'll probably look like a noob but whatever.
I think Zapdos deserves the S-rank it has for a few reasons. First off, it's extremely versatile. Zapdos is probably the most versatile pokemon in the UU tier after Mew. You say that its most effective sets are strictly offensive, but this isn't necessarily true. Its physically defensive set actually makes it a great switch-in to common physical attackers, including but not limited to Heracross, Flygon, Hitmontop, Ambipom (lol), Mienshao, and Crobat, all of whom were in the top 20 of usage last month. Jolly Heracross's Stone Edge does 45.43-53.75%. Even after Stealth Rock damage, that's only a 2HKO. Barring Crits, if played properly, physically defensive Zapdos can potentially PP stall Heracross out of Stone Edges. If you manage to rapid spin properly, Stone Edge is only going to be a 3HKO unless you get 2 max calcs that both manage to hit.
Subroost Zapdos is potentially the most annoying pokemon in the tier. It PP stalls every low PP move on any pokemon that's slower than base 100, and just roosts off any damage it takes. Another thing I'd like to point out, Zapdos is potentially a more reliable offensive Electric-type to use on your team because of access to Roost. Raikou has no way to heal itself, and is also vulnerable to all forms of hazards.
Looking at the usage stats for September, 71% of Zapdos were either Timid or Modest, so the only situation in which I'd consider my opponent might be using a defensive variant is if I see they're using a stall team. So really, Zapdos has Heat Wave and Raikou has Calm Mind, and for typically offensive Pokemon Calm Mind is substantially better.Finally, Zapdos has coverage options Raikou can't afford to run. Thunderbolt/Discharge is obvious on any Zapdos, but for remaining moves, you have to quess between HP Grass, HP Ice, Heat Wave, HP Flying, Toxic, and Roar. You can make an educated guess from the style of team you see in Team Preview, but you don't actually know what it's going to do. You might switch in Flygon only to catch a HP Ice for the KO. Or it could just be there to rack up hazard damage with Roar. I think Zapdos's coverage, and sheer versatility of possible sets should keep it up in the S tier.
Okay, about the Nidoqueen-Nidoking issue. It basically comes down to Nidoqueen's bulk vs Nidoking's Speed, since they are otherwise the same Pokemon. While Nidoqueen's bulk isn't significantly better than Nidoking's, it does help it considerably to check Heracross and Mienshao, which is a big deal in this metagame. Queen can also take an unboosted Extrasensory from LO Raikou and a Hidden Power ice from LO Zapdos while Nidoking cannot. The advantages of Nidoking's additional Speed are basically limited to outrunning Chandelure, because everything else comes down to a speed tie. The ability to reliably check 4 extremely dangerous Pokemon outweighs Nidokings capacity for outpacing Chandelure, in my opinion. Nidoqueen is not drastically better, but it is better, so I think it should remain in the A-tier and Nidoking should remain in the B-tier.