I'd like to post agreement with a few of the things posted so far, specifically, Greninja for S rank and Altaria for A. Greninja is just so good its not even funny. While it can't beat everything, obviously, it can beat most Pokemon in the game with the right move. Of course, it can't do all this in one set, but until you figure out what moves it has, it is nearly impossible to switch into it safely, and even then, the chances that you actually have a good counter for it are fairly low. With that said, it is frail and can be revenge killed fairly easily by scarfers or priority, however, before you even get the opportunity, it will probably have done some major damage. Altaria on the other hand is a Pokemon that does not immediately threaten like Greninja, but can, if played well, sweep large portions of teams on its own with very little need for support. Pixilate return hits really hard, especially when boosted. Furthermore, it can viably go either all offensive or bulky for its DD set, each of which needs to be handled slightly differently. What's more, it can also run a more defensive set and forgo DD entirely. However, unlike the Salamence that it tries to imitate, it can't just set up on anything. It also has big problems with guys like Skarmory and Cawmodore, plus many others if it goes mono attacking. Incredibly good, but not meta defining by itself. A perfect example of A if you ask me.
I would also like to touch on a couple of other mons I think are A rank.
First off, I'd like to propose Mega Gallade for A rank. Basically, it does similar things to Mega Medicham, but trading sheer instant wall cracking power for the ability to truly sweep. Its typing is absolutely wonderful for a physical attacker in this tier, as it is one of the few Pokemon able to fairly reliably take down both Tomohawk and Chansey, while also carrying good enough stats to break through other walls that take its hits neutrally, like Cyclohm. It does have issues with Reflect/Haze Tomo, but unless it is packing both, Gallade will be able to break it easily, and Tomo will always be scared to switch in. Beyond that, the good speed and Swords Dance let it be an impressive sweeper. The only real question with it is what move to run next to its STABs. It has a lot of options, and you really need to tailor it to your team, as each leaves it vulnerable to certain Pokemon. But with any of them, it is a fearsome Pokemon that teams need to be very wary of.
Secondly, another Mega I think is A rank would be Diancie. In a metagame with very few great mixed attackers, Mega Diancie is the best of them. Fairy + Ground coverage on the special side is nearly unresisted, and the few things that do are nailed hard by Diamond Storm. Like with Altaria, Skarmory can give it issues, but it packs such great special power that, despite its Steel/Flying typing, Cawmodore hates to switch into it (for reference, from full health, a 4/0 Caw is 2HKOd 20% of the time by 252 SpA Moonblast, assuming Sitrus Berry [On a funny note, that 20% becomes 0% with SR due to always having the first hit put it in Sitrus range]). Another neat thing with Diancie is the good bulk it packs before it Mega Evolves. I have more than a few times won battles by having Diancie not mega evolve late game in order to tank a hit from sweepers like Syclant and dispatch of them easily. This is especially notable on the special side if you pair it with Tyranitar or Hippowdon. As a last note, Diancie almost always will have a 4th moveslot you can play around with. Some people like Protect so that it can get its good speed unhindered. Calm Mind is also a good option to really pack a punch. Personally I've actually been using Hidden Power Fire. While this unfortunately costs a speed IV causing it to lose what would have been ties with Kitsunoh and others, it gives it an easy win vs Skarmory, a good move for threatening Ferrothorn, and a perfectly accurate option for picking off Syclant who are threatening to sweep. Overall though, its ability to clean through teams with just its main 3 moves is what makes this an A rank mon in my eyes. EDIT: Oh, and Magic Bounce. Forgot to mention that, but near immunity to crippling status is always amazing for a sweeper.