Yes and this is preference, which as I said, if you truly do prefer your control layout its fine, it comes down to preference but people are saying its "better". You cannot define something as better if all you have to back it up is your own preference.
I can think of two reasons, both of which you touched on. My guess is you underestimated how important these things can be for some people.
It isn't that much of an underestimation, it is more of a prediction that people are just not analyzing the controller correctly because human nature means humans are afraid of change, so they will look into all possible negatives to go against something that puts them outside of your comfort zone.
I don't have a problem with someone saying they like GC controller more because they are used to it and their hand just sort of knows it by heart. But saying the GC controller is better (as an affirmation) without a proper analysis is just not the right thing to do (in my opinion).
When the GC controller came out people were completely shocked at the position on the Z button, it seemed much more unnatural and everyone said it was wrong, yet today's controllers have no Z button, instead they have 2 L's and 2 R's and no one says anything anymore, because people noticed that it makes controllers much more comfortable to hold in your hands. (Even if you have to move your index to switch between both L's)
That's why. The position of the right control stick on the Wii Pro controller is strictly inferior compared to other controllers when performing aerial attacks using the c-stick. I'll show you why.
With this layout you're capable of using the c-stick for Dair, Fair, Bair with incredible speed while allowing you to reset your thumb position very quickly. Most people manually use their Uair with the other control-stick due to increase in speed, so you cover every aerial without sacrificing performance or comfortness. You're even capable of using Uair effectively as well since the button layout is to the left of your thumb so a reset is quick.
With the WiiU controller you're capable of using Uair and B/Fair depending on stage position without sacrificing anything. Dair'ing with the c-stick with this layout would be utterly terrible. It's possible, but overall you're at a disadvantage speed/precision wise compared to other layouts.
That's because that's not where your thumb goes, your thumb's neutral position changes to the Control Stick (which makes c-sticking in any and all directions much faster, natural and comfortable than any of the ones you showed). And thus by your analysis the Wii U Pro is strictly superior to the other layouts and using it puts you at an advantage speed/precision wise, Ill explain why.
You are trying to analyze the controller by using something you already know, this is isn't the same as another controller, it is different. Imagine your thumb being at the Control Stick. It makes using all c-stick commands much more comfortable as there is no movement. X and A button are still relatively close and have the same movement pattern as using the c-stick would on a gamecube controller. The only awkward buttons are Y and B. Smash only uses 3 face button. Now lets remember the fact that buttons are customizable on Smash and the fact that the "c-stick" is now in a much more comfortable (and natural) position. This itself is what makes the Wii U Pro actually superior by just editing your controls and not using Y or B buttons at all. (probable the best solution would be mapping jump to R or L)
Let's imagine mapping the jump button to somewhere else and just resting our thumb on the control stick, only needing to move our thumb in order to execute specials which we would have mapped to the X button. What this would mean is that while other controllers might be having you move your thumb from your jump button to the c-stick to perform an aerial this controller will allow me to just perform the aerial with no movement from my thumb (faster and more comfortably). And just as you move from the c-stick to the special button or the special button to the c-stick I can do that too, with just as much ease as you can. I can't see any downside.
- There is no aerial I can't perform faster or more comfortably than you.
- Specials have the same ease/difficulty in both controllers, except you move your thumb from south-west to north-east and I move it the other way around, there is literally no difference in distance or hindrances.
- With the new Tilt system Brawl introduced where Tilts are also doable with the C-Stick then Tilts are just equally as easy/hard to perform by themselves with both of the controllers yet... performing a Tilt after a Smash or an Aerial is much easier and comfortable for the Wii U Pro than it is for other controllers as you literally don't have to move your thumb at all.
- Just as an added bonus, my thumb rests on top of the Control Stick which is actually a more natural and comfortable position than the Y/X button which it will normally lay on other controllers.
Basically by mapping jump to a non-face button you are able to only have to move your thumb for specials, you don't have to move it for any other move at all. And even with specials you have to move it just as much as your opponent has to move it. (And that is only if he mapped specials in the closest button to the c-stick, since he has more face buttons to keep track of, his special button might not be the one closest to the c-stick and then you will also be at an advantage there.)
Try doing a comparison where you only use the X button and your thumb rests on the control stick, you'll see how your own comparison actually tells you that this controller isn't as bad as you give it credit and is probably better in terms of speed and execution (and comfortableness as it is much more comfortable to just rest your thumb where is naturally falls than having to switch back and forth so often).