Wobbuffet is totally uber for one main reason: SHADOW TAG
Any Pokemon can switch out to an appropriate counter if they find a Pokemon with both Counter and Mirror Coat. But Wobby prevents that. You may think that all you have to do to get around this is not attack Wobby directly, but use moves like Leech Seed and Toxic. But it gets Encore. This move screws you over because it allows your opponent 2 to 5 free turns to set up.
For instance, lets say Wobb traps your Blaziken and you decide to use Swords Dance, because after you max out your attack, you should be able to kill it in one hit. But Wobb uses Encore, forcing you to repeat Swords Dance. Then your opponent switches to a Belly Drumming Charizard. Since you are stuck doing Swords Dance, Charizard can Sub, Belly Drum, and sweep the rest of your team. Even if you switch out, your opponent still gets a free turn to do whatever he wants.