Here's the big problem with your objection, though: what are probably the 3 most-used features on the right thumb area of the controller? I'd say generally the Square/X button (commonly used for attacking), the Cross/A button (commonly used for jumping), & the right analog stick (commonly used for camera control). On the traditional layout, those 3 features are generally close to each other, making it easy to move your thumb between the three as needed.
Now, in Nintendo's layout, the face buttons closest to the right analog stick are Triangle/Y and Circle/B, the two buttons probably used the least in modern games. The two most commonly used buttons are on the other side of the face button diamond towards the middle of the controller. In order to fix this issue, you'd have to remap the buttons so Y and B are used for the most common actions, with X and A performing the least. Most games won't let you do that, and from what I've seen developers aren't remapping the buttons themselves to make them more natural for Wii U play.