I'm going to guess that motion controls aren't the sole problem with the game.
From what I can tell, the bigger problem is when you combine dual screen gameplay with motion controls.
As someone who took to the controls very, very strongly, this isn't a game that's going to go over well with the masses. It definitely isn't a game that'll focus test well, since the controls need to click with you for the game as a whole to work.
The way I see the controls is like this - almost all of the time it's like a traditional Star Fox game with gyro aiming: fly with the control stick, aim the crosshairs with gyro. Simple.
The "dual-screen" stuff is mostly contextual (though you have access to the cockpit view at all times), and the context is mostly forced. "Oh, you're engaging a giant boss? The camera on the main screen is going to lock you out of the view you want, so you need to switch to the cockpit view."
It's the excessive focus on the second screen as a key pillar of the gameplay (rather than a helpful tool when engaging large bosses with multiple destructible weapons/weak points, navigating tight spaces, etc.) that's throwing this game off. People get frustrated when they're forced to use it, and even worse
they feel like the game is forcing them to use it even when it's not.
Personally, I'd have nixed the cockpit view altogether, or at the very least eliminated it as an always-on feature of the GamePad, so people realize "oh, it's something that's useful in certain situations, but I'm not being pressured to use it." I definitely would have gotten rid of any forced usage when piloting the standard vehicles.