It's been a while since my last big post here, so let's get this going. I'm mainly going to react on most of the recent suggestions; a lot has already been said, but I'll try to add my own things.
Thundurus-I (S) → A+ | There's one really simple yet extremely major reason why I support the kami dropping: The metagame has shifted away from its favor. Don't get me wrong; Thundurus-I is still an absolutely fantastic Pokémon that will most of the time pull its weight, just much less than it used to. Pokémon like Mega Manectric and Latios have been on the rise, which can make life difficult for the kami: Mega Manectric can utilize Lightning Rod to absorb any Thunder Waves or Thunderbolts that Thundurus-I uses and raise its Special Attack to become a huge threat after Mega Evolution, while Latios has no trouble at all switching in on any of its offensive moves. In a metagame where hard hitters are everywhere, Thundurus-I can't exactly thrive well, either, thanks to its pitiful bulk.
All in all, while a great Pokémon, Thundurus-I is nowhere near as metagame-defining as it used to be. Drop it to A+.
Latios (A+) → S | Latios is magnificent in the current meta. Its versatility, flexibility and adaptability to just about any kind of team is just astounding: it's bar none the best offensive Defogger in the tier, is an excellent attacker due to the large variety of offensive sets it can run; this enables it to combat a huge amount of Pokémon in OU. Despite the large choice of moves, Latios doesn't suffer from 4MSS, since its team can easily cover for any blind spots in the coverage it runs. This brings forth a factor of unpredictability as well; you don't know which offensive moves it'll run aside from Draco Meteor, so it's all a big guessing game until it reveals its moves. It's unfortunately still Pursuit bait, but with Tyranitar's usage on the decline and the metagame overall shifting to the dragon's favor, Latios is a near-flawless Pokémon as it currently is. It's the best Pokémon in OU. No doubt about that. I feel like its ranking should reflect this position as the absolute best, so Latios should rise to S.
Mega Gardevoir (A) → A+ | I'm really glad it's been brought up again. I feel like some people are really underselling Mega Gardevoir's qualities, namely pressuring defensive teams with its amazing offensive prowess and even giving offensive teams a hard time due to its incredible power. The current state of the metagame is more favorable to Mega Gardevoir than it was before; with Pokémon such as Latios on the rise, which it can check quite easily, as well as Pokémon that can support it well seeing more use, things are definitely looking bright for Mega Gardevoir. Magnezone can trap and KO Steel-types, which are pretty much the only thing giving Mega Gardevoir a lot of trouble, while in return, it can beat some of the Fighting-types that plague Zone. I haven't heard much about the defensive set yet, but I guess it does add more unpredictability to Mega Gardevoir and makes it usable on more kinds of teams. It's just great in the current meta, so it wouldn't hurt moving Mega Gardevoir up to A+.
These were the main suggestions I was gonna stand behind. I'm really on the fence about most others, but I'll list each of them with a very short explanation.
Mega Charizard X | This thing remains a threat to lots of playstyles, but I will admit it's lost its touch over time and it can't exactly find the time to set up on fast teams, not to mention the rise of Rain Offense being harmful to its Fire-type STAB. Sand Offense still hurts it really badly, too. Despite that, though, its Fire/Dragon-type is still incredible and has nigh-perfect, high-power coverage. It can still perform its three roles excellently, just not as excellently as it used to. In the end, I'm fine with it going either way, be it falling to A+ or staying in S.
Azumarill | An excellent Pokémon that's just amusingly easy to slap on teams and has a variety of highly usable sets, but as somebody has pointed out before, none of these sets are really mind-blowing and have some serious flaws. You really have to choose between power and bulk when using Azumarill and while it can fit on a large series of teams, the difference in power and bulk is really noticeable. As with Zard X, this one can go either way.
Just as a final suggestion to spark some more discussion, would Mega Manectric be good and dominant enough to rise to A? It's a highly reliable Electric-type that can do a whole lot on just one team slot and pairs well with many common Pokémon, particularly forming an excellent dual-Intimidate VoltTurn core with Landorus-T. Mega Manectric is one of the best switch-ins on Steel-types; Mega Scizor and Magnezone are both fried by Flamethrower and can't do a terrible lot back. I dunno, it sounds good enough for A in my opinion, but A- is already a good place for it to be.
Also drop Zapdos to C+, it's just bad in the current meta. Latios is ever more common and entirely eclipses it as a Defogger, while both Mega Manectric and Magnezone are better Electric-types and are far better at what they do than what Zapdos tries to do. Sucks as a Flying Spam check compared to Rhyperior and Mega Aerodactyl, too.