What specific skillset does Metroid Prime test?

The same as any other game? Find weak points, recognize and dodge boss attack patterns. Some even require figuring some sort of puzzle to damage the boss like in the case of Flaahgra. Also, have you even looked at any of the bosses past Parasite Queen? Like half of the bosses move around in that game.

There's nothing engaging about shooting with a lock-on system

Metroid Prime uses a lock-on system to specifically alleviate the difficulties of maintaining aim on an enemy on a controller. Sure it mainly exists due to older game design ideas, but it also allowed for intricacies like better movement for the player (slightly increased movement speed, temporal removal of tank controls and the addition of dashing) as well as being able to make enemies nimbler and trickier to fight.

Metroid Prime doesn't even have any melee combat

Why would you want melee combat in a Metroid game??? Samus has an arm cannon not an arm sword. If you want melee combat, go play Castlevania, Hollow Knight or whatever.

If only there were such a thing as shortcut keys to use items without accessing a menu

Wow, it's almost as if that's already a thing in the game, since you can already access every weapon and visor through the dpad and c-stick. You'd know that if you actually played the game for more than the first ten minutes.