There are a lot of possibilities with the controller, some games will use it in a lot of unique ways (most likely only Nintendo games) and it will be better for some genres than others, FPS won't probably use the controller in any way other than a map or inventory, but imagine the possibilities for puzzle games. Also the Wii U could be the first home console that brings a real MMO.
As for how comfortable the controller will be, well Nintendo isn't stupid (for the most part), they won't make something that hurts your hands after long periods of time, and for what I heard the controller is really light, so that shouldn't be a problem.
The problem is that "hardcore gamers" will just bash the system no matter what, most of them are just blinded by their own fanboyism for the other consoles, and it doesn't matter if the system turns out to be a really powerful and awesome machine, those "gamers" will still make stupid excuses as for why the system sucks...
Nintendo and PC gamer
