...we'll have support for Wii U Pro Controller in the first update, it's coming in mid-December or so. The reason for this was pretty simple - we just didn't have the controller until a week ago, so we couldn't add support for it, I think Nintendo had to send all their samples to retail games or something. - Joel from FrozenByte
Well, that's a silly but believable reason! Just good to know that it'll be added in soon enough. Thanks to Dax for the heads up!