Use Empoleon more.
It switches into Choice Latis twins with ease (watch out for Thunderbolt, and obviously, Calm Mind), doesn't mind taking a Choice Band Dragon Claw from Garchomp, or Outrage in a pinch. It loves Bullet Punch from Scizor, or any Choiced Skymin spamming Air Slash (watch out for any Skymin not stuck in Air Slash, obviously). It requires prediction to use, but with all the Choiced Pokemon now, everything requires prediction.
As for other suspects:
Shaymin-S:
Used: Yes
Shaymin is a beast, and I don't find it as horribly frail as some make it out to be. SubSeeding works wonders in this metagame, although you must be wary of all the Scarf sets around. Aside from my use of SubSeeding, I've seen Choice Scarf, and Life Orb variants. Life Orb, in my opinion, being the most straight up deadly. SubSeeding works, but must be setup for it. Choice is the least effective in my opinion.
Garchomp
Used : Yes
Scarf is in. And it will probably remain in now that Garchomp is not the 'fastest Dragon in OU'. Earthquake is a lot more risky now with all the floating Dragons. One wrong move matters more than ever before. With Garchomp rarely having time to setup Sword Dance, and then not outspeed a lot before the rare SubSalac et, he is not 'quite' as threatening. Every Garchomp, aside from one all out attack, I've seen thus far has been Choice Scarf. I think Latias and Garchomp to co-exist in the same tier, I'm not too sure about..
Latios
Used: Yes
Very powerful, indeed. Not a lot enjoys taking a Specs Draco Meteor to the face (hello, Empoleon..). And those that can take it are defeated by Thunderbolt/Surf.. or in some cases, Grass Knot depending on the set. He is somewhat kept in check by revenge killers, and being weak to Pursuit, but the extra power over his sister is obvious. And deadly.
Manaphy
Used : No
The few I've seen have not performed well. One was a Tail Glow set of some sort, but died to Scizor U-Turn+Skymin. The other tried to Energy Ball Empoleon to death, which did not work out in its favor. I thought Manaphy was OU before, and this test will do little to change it. Manaphy IS very powerful, but this is not a favorable environment for it to shine.
Latias
Used : No
With the hyper pace of this metagame, I don't think Latias has much of a use, unless you're trying to pull off the ol' Double Special Dragon. But I yet to see one of her, so I can't comment.
Deoxys-S
Used : No
The few leads I've seen have been annoying as always. My Scizor is especially meant to take care of it, but that's not always the case. Deoxys-S ability to not have to suicide in the beginning of a match, setting up screens multiple times is a huge pesk. I've yet to see someone try it as a late game sweeper, but I've no doubt it cleans up like nothing else.
Other Pokemon:
Scizor is a handy lead for me right now. He can take care of most Deoxys with Brick Break to shatter the Screens and U-Turn, or 2 Bullet Punches to take care of him once and for all. On a Screener set who does not invest in Attack (assuming speed, and HPs), Scizor Max HP Scizor has no issue surviving Fire Punch.
Tyranitar with a lot of Special Defense works wonders right now. With everything sporting Choice items, he easily finds time to switch in and crush everything into KO range for the rest of the team.
And as mentioned, Empoleon is a great Pokemon for this game. It threats all the Dragons with Ice Beam, and makes it hard for this very offensive metagame to switch in on three attack and Roar.