Sleep Talk Kyogre is not a Darkrai Counter, I never said it was. It makes a decent check, being able to OHKO with Rain Boosted Surf with little investment and a positive nature, I know the standard is easily capable of doing it. Besides, Darkrai, as its analysis says, is most vulnerable when sleep clause is in effect.
As for Darkrai carrying Substitute, yes, it is very dangerous, but Darkrai has moveslot syndrome on non-choice sets. Assuming a non-choice Darkrai (one could argue trick in itself is a threat to stall teams) has one of the following moves, Dark Void, Dark Pulse, Nasty Plot, Focus Blast and Substitute, regardless of what it chooses to omit, it will still have problems. Dark Void is what makes Darkrai threatening, allowing it a free turn of set up, Dark Pulse is a required STAB, Nasty Plot allows Darkrai to use that free turn to its full potential, Focus Blast is required for Type coverage and throwing a sub into the mix means losing on one of the previous moves, which restricts Darkrai. Without Focus Blast, it'll lose to Blissey, Dialga and T-Tar bar some Hax, dropping Nasty Plot means it has no way to take advantage of the free turn, other than hoping to nail something on the switch and dropping the other 2 moves go against Darkrai's very nature. Once you see the sub, even if you fail to break it, you'll know its limited in what it can do. Besides, the non-CM resttalkers do fine, with a 2/3 chance to break the sub, slightly less factoring the 1st turn wake
Hm, I think a new Project Uber could be useful. Sadly, I don't think I'll participate, I haven't even shoddied for a while, or even used my DS for anything lately short of the Shaymin Event, but it'd be great to see Ubers diversify a bit. Hell, if I can get some spare time, I'll even do some testing.
Many players also come up from OU trying to Counter everything. Ubers isn't about counters, thats why everything is Uber, its too much for almost everything to handle. A good Uber Team checks as many threats as possible.
As for Wobb, not counterable, but I get what you mean by working around it. If I use a strong U-Turner, I always pack a ghost. Still nothing counters Wobb, as nothing likes being Encored at the very least. Also, putting unpredictable moves on something is always a good way to eliminate Wobb. One of my teams has Roar on Latias (I use it mainly as a lure to ease a Darkrai Sweep and my other Lure already has HP Fire), which can allow me to escape Wobb's clutches, just because people predict a Meteor