For mixed sets (or unable to predict attack VS Set-up), Destiny Bond might be an option. And if it could force opponents out of attacking next turn, (if a pair of moves like Palkia's Surf+Aqua Tail would 2hko and you don't know which one will come first, and you foe tries to outsmart you, he is still screwed if you use Destiny Bond the first turn) this way you can use Encore the second turn *the foe will be more cautious to not activate it*, and then you switch to a set-upper the 3rd turn...
Or say you don't know if a Groudon will use Swords Dance, or Earthquake (Earthquake is a 2hko, or 1hko w/ Swords Dance), and the first turn you use "Destiny Bond". You didn't waste a turn Encoring Earthquake (and dying the 2nd turn/switching out for nothing), nor did you use Counter on Swords Dance (and dying the 2nd turn/switching out for nothing). With Destiny Bond, if Groudon uses Swords Dance the first turn, he will definetely die the 2nd turn if he uses EQ, or he will have to try and outstall your Destiny Bond by using Swords Dance again, in which case he will be Encored. If he used Earthquake the first turn, he knows your Destiny Bond will Ko him next turn if he does it again, so if he switches to Swords Dance, you can Encore him.
So Ultimately, on the 2nd turn, he will either kill himself with Earthquake, or get Encored, say into using Swords Dance again, then you can switch and set up. Whereas its a guessing game with relying on Counter OR Encoring at the right time. Making Destiny Bond turn prediction towards your favor, making your opponent have to guess when you will Destiny Bond.
Most Groudon with Swords Dance are Paradance Groudon - they have Thunderwave. Wob will probably end up paralysed, and it will probably end up using Encore on Thunderwave. Few of the pokemon you would send in on Groudon will enjoy being paralysed. Plus you will eventually end up calling your cleric, for Wobbuffet cannot afford to lose a turn to paralysis. Safeguard seems to be the better move against Groudon, for it protects your team from Thunderwave and Toxic.
The beauty of Destiny Bond is that Wob is so slow, it will last the turn after its used, so it will KO your foe the following turn depending on their move, while you can safely use Encore, since it will go after their move.
Wobbuffet being so slow is the reason why Destiny Bond is never used.
Additionally, using Wob. as a lead could be interesting, against, Kyogre leads, you could even just use Wob as bait for Kyogre to use Water Spout/Surf (since it will be Mirror Coated with Thunder/Ice Beam), and switch to a Water Absorber/Parasect/Palkia/Ludicolo, allowing for set up. This is relevant to Wob keeping Kyogre trapped, so you can safely get your switch in to say Ludicolo, and threaten a Swift Swimmer Sweep.
On this topic, only Specs Water Spout will OHKO Wobbuffet. But predicting what item your opponent has is far too risky, so yes, sending in a Water absorber can work. Alas though, Wobbuffet already requires team support to be used to its full potential. Do we really want to use up another team slot just for Kyogre and just to have a Wobbuffet lead.
Additionally, Wobbafett might attract Taunt from Deoxys-S leads (they don't want to get Encored into Stealth Rock and then Tickeled to face a Putsuit Tyranitar (nullifying their Focus Sash with Sandstorm and Koing them on the escape), and if you predict the taunt, you can just switch to a sweeper that doesn't need Set-up.
Sending in a Tyranitar (or Weavile) onto Deoxys-S is very risky. It commonly has Superpower, and it will OHKO. And by the way, the standard Deoxys-S lead wouldn't Taunt against Wobbuffet. It would just set up Spikes.
In other words, play with Wob's other options. Destiny Bond doesn't seem like such a bad idea if it can make predictions alot easier. Tickle I guess could work on stall Pokemon, especially on Lugia/Giratina when combined with Encore, where Pursuit will be Super Effective to really get past their defenses.