As nice as some of the Deo-D lead sets are that some of you guys posted, I would ask you to keep in mind that this thread about posting methods of stopping Deoxys-D set up, not about Deoxys-D in general.
Anyway, I wouldn't consider using a slower Choice Band/Choice Specs user necessarily "beating" Deoxys-D. Deoxys-D "only" gets to set up SR, but by being locked into one move, a sweeper can much more easily set up on you. This is really a position the Deoxys-D user wants to achieve (albeit they would prefer it with one layer of Spikes) since it has SR to weaken most targets sufficiently. If your faster at least you allow your next switch (and all upcoming switchin's) to take on the target at full health.
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Originally Posted by Fat alexwolf
And again, what is so broken about a guaranteed SR, if it means your opponent losing a poke?
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What really makes Deoxys-D different from other leads for offensive teams who can consistently set SR up, like Aerodactyl, is that its sheer versatility makes sure once you send out your stop at turn 1, you can't be assured that it won't be the variant that will screw you over real badly. Anyway here are two other sets that I found can handle Deoxys-D nicely.

Gliscor @ Toxic Orb
Trait: Poison Heal
EVs: 248 HP / 44 Def / 216 Spd
Jolly Nature
- Earthquake
- Substitute
- Baton Pass
- Taunt
Of OU CCAT fame, SubPass Gliscor can take advantage of Deoxys-D leads to create a Substitute for other team mates to utilize as a buffer against the offensive teams attacks. However you sacrifice bulk in order to set up on Deoxys-D. However, if the opponent fails to send out Deoxys-D, you can use Baton Pass to get a better matchup just like U-turn. It is pretty rare for Gliscor to run a faster Taunt than Deoxys-D, so it will surely catch a few opponents off guard.

Durant @ Life Orb
Trait: Hustle
EVs: 252 Spd / 252 Atk / 4 HP
Jolly Nature
- X-Scissor
- Iron Head
- Superpower
- Stone Edge
Durant is one of the few Pokemon who has a very good chance of OHKO'ing Deoxys-D without locking itself into a choice move. While Durant is very powerful, it is unfortunately hindered by Hustle's annoying 80% accuracy penalty. In addition, Durant faces stiff competition for an offensive Bug/Steel type from Genesect and Scizor.