Because a third-person shooter like Splatoon is not a first-person shooter, and Metroid Prime's FPS multiplayer was only in MP2, supported a maximum of four players, and by all accounts (never played it) was rather lacklustre. Now if they wanted to bring back some elements of Metroid Prime Hunters multiplayer, it'd be extremely barebones but at least it would add variety to their library.
My grievances with CoD is how twitchy your fingers need to be to play, let alone win, and why I'm a bigger fan of boomer shooters like Halo/Quake that are slower paced, and more so why I appreciate TimeSplitters/GoldenEye/(I think Perfect Dark?) is that you were allowed to carry more than two weapons at a time for true chaos, along with health paks, armor, and map spawned equipment/power ups, and even as something as simple as bots so you could play the multiplayer solo