I feel like I'm the only one who prefers the original, gamecube controls. Playing through the switch remake, I played with the new controls for, like, 10 minutes before switching to the original control scheme and playing the rest of the game with it.
I'm with you on the Gamecube controls, tank controls are awkward but Wii pointing is more awkward. Although the best control scheme I used was a Steam controller on Dolphin (for the Wii version).
The Wiimote worked with a pair of IR blasters to locate your screen. Joycons have no idea where your screen is. In that light, that they work as pointing devices at all is actually rather impressive.
Oh man, Wiimote and nunchuck on Metroid Prime was incredible. So goddamn intuitive. You just... point at everything. I've actually been holding off on the remake because my one and only playthrough of MP1 was with the wiimote. It ruled.
I forgot what the setting was, but the mode with the littlest deadzone/bounding box was the way to go for me. Had the butt of the wiimote rested on my leg for stability and played the game like a joystick aimed at the TV.
With Primehack you can play the OG prime series (I think the Wii U version?) on PC with a controller for dual joystick control like a modern FPS, or even m+k. It also runs well on steam deck, I have it on mine. It's very excellent, highly recommend.