Just my 2 cents on this discussion.
I don't usually post in smogon, even though I have an account. But then I realized. Why not? If I can influence the discussion in any small manner why not take a stab at it?
So on with the view...
Though this may not come out right. but Deoxys-D has no 'true' counter.
Let's see what counter means:
"A counter is a Pokemon which can reliably stop the opposing Pokemon from doing it's job."
What is Deoxy-D's job: Hazard Setting.
Can anyone stop it at that?: Not really.
It can almost ALWAYS reliably get hazards out. Multiple Layers at it. It was kinda
nerfed in the Gene era, as lead genes could reliably KO it with a download boost, depending on their Set, or at best set it up for a 2HKO by U-turning in a appropriate Scarfer/Bander limiting it to one layer Now with him gone, this thing just runs rampant.
Lets Consider this. The two of the Strongest Bugs in OU: Scizor and Volcarona both fail to OHKO it reliably, so even if you lead with then it will almost always get rocks out.
The Specially Defensive Variety even survives Specs/Quiver Dance Volcarona at +1 (can't boost any more thanks to taunt). Bug Buzz will do a MAX 99% considering all favorable conditions which is damn impressive, considering it has a monster 400+ SpAtk Stat to begin with.
252SpAtk +1 Swarm Volcarona (+SAtk) Bug Buzz vs 252HP/252SpDef Leftovers Deoxys (+SpDef): 83% - 99% (254 - 302 HP). Guaranteed 2HKO.
Bulkarona which is more common in OU and depends almost exclusively on Quiver Dance and Fiery Dance to get it's Stats up don't do much.
I believe many people have already done the Scizor calcs.
What's worse? Red Card.
Which can Effectively ruin your game and let it set up MORE layers as you're helplessly switched out to a pokemon you don't control and you essentially give it 2 free turns 9/10 times.
is technically the only thing which can OHKO it in OU, without letting it set hazards, (and even LO cannot
if it's the Purely Specially Defensive set) and we all know what kind of usage it is getting (around 5% as of the latest stats and around half of them using LO and are Mixed).
is slower so it will always get rocks up at the very least, but Maximum T-Tars in OU are the Bulky Weather Warriors with a mixed set, which again is incapable of OHKOing Deo-D.
Let us consider the other Options? Taunt it?
For a Defensive behemoth it has a very broken Spe stat of 90. Couple that with it's own taunt and Magic coat (and the somewhat uncommon Mental Herb) means that your chances of Success with that strategy is very slim.
Again. It also has the very Fearful skill swap which will make it more dangerous than it already is if you somehow end up gifting it a permanent magic coat.
Set Up on it's face?
Nah. Taunt obviously stops you from reaching more than +1. That and you need an insanely strong SE+STAB attack in the first place to kill it. Not to mention you have to chance of being switched out thanks to red Card leaving you with no boosts and Deo-D's team with all the hazards.
To summarize (tl;dr version
Deoxys-D has no true counters
. But all it's Sets have certain checks. But even having said that it doesn't have any true 'universal check'. It can throw hazards at you face without any drawbacks for it will not be taunted and will certainly not be treated as set up bait. It's the defensive counterpart of Gene. All the sets are counterable but you never know what it is carrying. If Genesect was found Uber for that Reason alone, Deo-D certainly deserves a very thorough suspect test.