If I have a silicone cover fitted to the gamepad, will it still fit in the charging dock?

It should do. I got a blue cover:

Yes I know, the screens dirty as hell again. Luckily when it's switched on you can't see the dirt screen.

no it doesnt fit well in the charger i know i tried.. it wont touch the contacts

I bought one that fits perfectly with the dock.

http://www.pdp.com/p-1325-silicone-jacket-for-wii-u-gamepad.aspx

I guess worst case, you could cut out that section of silicone yourself.

@GeePers - good to hear it worked for you.
The silicone skins they sell locally here look like they are quite thin and I think it might just work.
@Bass - dirt + grime on the black gamepad will drive me nuts, that's why I need that cover. The thing gets dirty from me just looking at it

Thanks for all the responses, much appreciated.

Well the one I have stops the cradle charger from working but with kids I am happy to just plug in the cable to charge it compared to having their dirty hands all over the actual black gamepad

Where do you get those silicone covers?

Will those protect if from dropping like the Wiimote jackets did? I ask this cause with kids you can never be to careful.

Depends... probably good enough if you dropped it a foot or two onto carpet. Dropping it from the International Space Station not so much. The silicone isn't nearly as "cushiony" as the Wiimote covers, but I figured with kids I was better off having it on. I got mine at Best Buy.

The one I have does, simply because there is no silicone at the bottom where the pad fits into the charger.