Play Metroid Prime for Wii U just using gamepad

Metroid Prime Trilogy uses a Dual-layer disk, which some (older) Wii consoles have trouble reading.

Most likely, the source of the problems is a dirty lens, which may be solved by using the Wii Lens Cleaning Kit.

Alternatively, You can contact Nintendo, as they are aware of this problem and (usually) repair your Wii for free.

If you fire a regular beam charge shot and then immediately hold down the missile button, you should be able to start charging the seeker missile without having to "waste" a shot.

The key is to begin holding down the missile button during the "cooldown" period of the charge shot animation (when you are unable to fire anything, beam or missile).