Whatever their reasoning was, it was ultimately Nintendo's decision. Like I said, I couldn't have cared less about the inclusion of Wii U gamepad features, and the majority of Switch owners probably agree with that. It matters very little in the long run because this is the last game released on Wii U, and obviously Nintendo won't be going back to dual-screen home consoles if Switch sales keep going at their current pace.
What an idiotic comparison to make. Gaming does not require knowledge on how to operate military vehicles. Right trigger to accelerate, left trigger to brake. The vast majority of people playing CoD are in no physical shape to pass basic training, let alone have the mental capacity to learn the intricacies of jet operation.
Of course, there are highly complex and detailed flight simulator games, but these are extremely niche. If you released a console that came with multiple switch/instrument panels and multiple displays and multiple operational sticks, and then made it a requirement to use all these things in every game, guess what? It would be very pricey, and it would sell like shit. Just as Wii U did.