Heat Wave is actually a big deal. It lets you get by Roserade and Shaymin, pokemon who check Raikou that lack HP ice. I've already acknowledge that Raikou is a better sweeper, but as an attacker (and a pokemon in general) Zapdos is better. On top of obliterating everything, it can actually switch into the most potent physical attacker in the tier (Heracross) and it has recovery.
Let's assume the Gen 4 OU Sub CM set for a moment. Using that, Raikou can set up at least two Calm Minds on LO Shaymin, as Earth Power deals less than half on the first CM. Roserade switching in on Raikou just allows it to boost more. At +3, LO Sludge Bomb stops breaking its subs and Tbolt gets an easy 2HKO. Leftovers variants of these Pokemon are complete setup fodder and Raikou can actually CM right in front of them on the revenge.
For exaggeration's sake, Raikou can 'obliterate everything' too with a simple CM Life Orb set, but it's usually less popular than Sub CM due to its gratifying lategame sweeps and ability to bypass even faster checks under the right conditions.
Also, if I were you, I would avoid switching non-defensive Zapdos in on Heracross as much as possible. Adamant Scarf can 2HKO you with just its STABs after rocks and CB puts you in SR range where you're forced to attack and can't bring him back unless you get off a spin. He can revenge Heracross or force out Scarf it it already got a kill, but that's about as far as it goes.
Nobody uses Clefable (and for good reason, its not that good) and its taken any prior attacks, it will be 2HKOed. Deoxys-D isn't beating Zapdos without special defense and toxic... but why would you want to do that? Umbreon is not impressive in the slightest. though i'll admit Porygon-2 and Snorlax are fine checks. So really, Zapdos has 2 relevant checks, 1 of which can easily be worn down by Spikes. Nevermind the fact that Raikou is checked by Scarf Krookodile and Flygon. Neither of those Pokemon can OHKO Zapdos, so Zapdos has no problem roost spamming (though you risk getting crit) and Stone Edge is a shitty move to lock yourself into. Even Rhyperior can check Raikou since its less likely to run HP grass.
You're placing too much weight on usage and relevance in a relatively balanced tier with so many options. One of the reasons it's hard to keep a consistently high score while laddering in this tier is that there are just so many dang surprises. Every other match is a new set/hidden gem that you didn't take into account when building the team. For example, do you realize how many teams are Galvantula weak these days? Preparing for the top dogs doesn't cut it anymore, you really do need to be ready for
anything. I'm still on the lookout for that million-dollar combination myself.
As to why you're wrong about Clefable, it's much better now that Chansey is gone and fits perfectly in a hazard-obsessed metagame. A simple Encore set can beat most CM users, and wearing it down is simply not an option due to Magic Guard. As far as I'm concerned, it's as legitimate a counter to Zapdos as any other decent special tank.
Specially Defensive Deoxys-D is a huge roadblock to a lot of special attackers, including Zapdos, and a much better team player than his faster sets. All it needs is Taunt to prevent the Roost while its Tbolts fail to even 3HKO Deoxys. No Toxic necessary; Deoxys wins no matter what unless it's SubToxic, which is beaten by a lot more than Deoxys.
No you misunderstand, I wanted you to tell your choice for #1. (my fault for shitty wording!!!) I disagree with your opinion btw, I think Zapdos is far ahead of those threats (Raikou and Roserade are at least) debatable.
I probably should have said this earlier, but at this stage of UU, I don't think there is a legitimate king. The closest we have is Roserade, who is by and far the hardest to switch into of the above, and can influence an entire match with both of its most popular sets, regardless of checks on the opposing team. The saving grace, I think, is that its defense is crap enough to leave it vulnerable to Pursuit without even being Pursuit-weak and it doesn't quite hit the 100 club, so it has a few decent checks if you predict correctly. But still, with the hazards, immense power, coverage,
and reliable Sleep move, most people will struggle in beating him more than they ever will Zapdos.