The main problem with the Wii U Gamepad

[Iyasu]

The main issue is it is of no use to many genres.
For fast paced games you do not have the time to look at the Gamepad. It has no good use in platformers, fighting games and action games, and most games on the Wii U were from those genres.
In genres like racing games it could be useful as a back mirror, but the Wii U isn't powerful enough so the graphics have to be scaled down to support that.
The genres it is useful for are games with heavy inventory management, open world games, RPGs and the likes, and there were too few of those on the Wii U.
It is easier and faster to touch a screen to manage your inventory (Deus Ex, Zelda) or fast travel to your destination (Xenoblade X, Splatoon) than to select the destination per menu. You can draw or drag and drop things around (Miiverse, Mario Maker) You can also type quicker with an on screen keyboard than with a standard controller (apps, scribblenauts, "enter your name").

In short:
The biggest issue with the controller is, there weren't enough games that benefit from a touch screen.

I also believe the people that hate the controller mainly play games from the genres that don't benefit from it, while those that like it enjoy those genres that benefit from it.