In a few experiences I've been using Wynaut I'm seeing that Pokemon like Infernape are doing more damage to stall teams than Wynaut is. Running Custap Wynaut with Destiny Bond, Encore and CounterCoat seems to be one of the the best thing the little bugger can do. Even resisted attacks to tons of damage to it unless you forgo speed for defense, and if you do that you're missing important outspeeds like Blissey.
Wynaut is frail enough that it hardly gets to countercoat, it's so slow it takes little extra bulk it has away to outspeed anything so Encore isn't as useful either, its ability to Tickle, Safeguard, or Destiny Bond (even with Custap) is severly limited by the fact that it's difficult to stay alive.
Wynaut on his own is pretty bad. Coupling him with something like NP ape setting up on Blissey Wish Encores or something is what people are looking for in Wynaut, I understand, but he's not like Wob. You can't Mindlessly do this multiple times like with Wob. You can do it once a game, and you has to be careful about it. That's the big difference. He can only come in on REALLY slow walls or ones with no real attack power (only an attackless Skarmory comes to mind for that second part, though) and use them as set up bait, either that or on someone stupid enough to use a non-damaging move on you. He's just so limited on how to get an approach on a free move for a switch-in compared to Wob.
I'm not seeing reasons to keep Wynaut Uber so far. You're either too slow to do anything but can take two hits, or too frail to take two hits but fast enough to lock a wall into a move. Maybe Wynaut could be fun on a Trick Room team or something, but even that doesn't sound plausible.