Well, let's say for the sake of simplicity that Layer 1 is the physical aspects of wifi 5GHz and Layer 2 is ethernet.
I don't see why you would change any of that, it seems to work fine : multiple wifi devices do work without shutting out each other, unless there is a lot of congestion. It all works already ; 802.11 n even allows devices to use multiple channels for the better or the worse, or at least seamlessly switching between them to manage to get the packets across.. if I'm not mistaken.
If you manage to suffer too much congestion so that your Wii U gets unusable, well, bad luck. It shouldn't happen : 5GHz waves have a harder time crossing walls and obstacles, and 5GHz wifi has a pretty wide spectrum.
Then using something other than TCP/IP is absolutely no big deal I think. I remember ~10 years ago when I had TCP/IP, IPX (for games such as doom2) and NetBIOS all on the same 10Mb ethernet network (we had two 98SE PC, one XP and one 3.11)
Using a custom, non IP protocol is worth it : there would be absolutely no downside to it and whatever gains in latency, better sized packets, simplicity you get are free gains.
According to wiki they are using the 5Ghz spectrum which is different from the 802.11n spectra (which uses the 2.4 Ghz range) and some type of proprietary transfer protocol. The technology seems to be the same, just using a spectrum that currently no off the shelf wifi device uses.
This tells me that they took 802.11 and customized it to the 5Ghz spectrum to take care of the first two layers, and they customized the third and fourth layers to their requirements as they would not need the complexity and functionality that TCP/IP stack provides.
So yes they customized the whole damn thing, for the better or worse.
Isolating the WiiU wifi network by using 802.11n technology on a complete unused spectrum would solve pretty much all the congestion issues it may have in contrast to using the standard spectrum.
Of course today's wifi has plenty bandwidth to stream compressed video, there's no doubt about that.
However, the problem with using the same wireless spectrum is that wireless uses collision avoidance.
Two devices cannot transmit on the the same channel at the same time, or else you end up with destroyed frames. (also the reason it's half-duplex) Yes you could use different channels, but the amount of channels in the 2.4 Ghz range is limited, and you cannot control how many channels are being taken and "abused" by other devices.
The problem occurs when you have some devices in the existing wifi environment transmitting a shitload of stuff (think conferences), thus you would want to use a complete separate unused spectrum to maintain reliability and limit interference.
I'm kind of getting lost on the direction of this discussion, but anyway, based off of the current information we probably won't see people hacking some router or usb wifi stick to communicate with the game pad as the devices are already incompatible from the first layer.