There is not a single doubt that GamePad is superior to JoyCons.  It's generally more cramped and less ergo.  The full size Wii U analog sticks beat the JoyCon's analog sticks.  The offset analog stick on the right JoyCon is bad for handheld gaming mode.

https://www.youtube.com/watch?v=8GsXbuR23WU&feature=youtu.be&t=114

That's a good video summarizing ergonomic issues with controller, I recommend it for anybody not "grasping" issue (har har).

Nintendo should have bit the bullet and switched to symmetric sticks if that would minimize ergonomic issues for tablet controls.
In order to avoid confusion they would also need assymetric Pro layout as well, even though it is not particularly needed there,
but that seems the right choice to have made, rather than worst possible ergonomics that will impede longer duration tablet play.

The choice to prioritise simplified visual design over ergonomics on the "dog face" JoyCon adapter was also poor IMHO.
The 90 degree / vertical alignment carries over poor alignment from the tablet, whereas angling the JoyCons relative to vertical
(or even in depth as well) would allow for both analog stick and buttons to be equidistant from natural "neutral" thumb position, 
thus easier and more comfortable to use with natural hand posture emphasized by beefier palm grips of the "dog face" adapter.  
That trivial difference would allow MUCH closer ergonomics to Pro controller, but Nintendo just couldn't manage that.

I've mentioned in other threads I see high likelyhood of 3rd parties releasing "grip augmenter" shells to improve hand position,
which would at least allow similar ergonomics to "dog face" JoyCon adapter, if not "actually good" ergonomics of Pro controller.
It also seems like there is viable market for replacement tablet controllers that are larger but offer ergonomics on par with Pro,
basically good hand posture AND alignment of analog sticks / buttons , not simplistic vertical alignment like standard JoyCons.

People on Neogaf are reporting even worse framerates on later areas of the game on the Wii U version.

I mean I guess it's not surprising on Wii U. They need to patch Switch version ASAP to address frame rate in docked mode.
If necessary that just means dialing back the docked mode's graphics upgrade so it can offer same FPS as portable mode.
Seems like it should be addressable with some better optimization and GPU hacking without lowering level of graphics.
(which of course are still not 1080p even in docked mode)

I guess it's early days yet and Nintendo will get much better at optimising. But BoTW struggling to maintain 30fps at 900p is not terribly encouraging for people who prefer Switch as a home console. Docked mode for any game should always provide the better experience. So was it a bad decision by Nitnendo to make Docked mode render at 900p and sacrifice framerate because of it? Does Nintendo regard it as unacceptable for a game to output at 720p in docked mode and thus higher res must be achieved even at the expense of other performance elements?