That's sort of the consequence of very few returning characters in the context of a multi-series crossover. It's easy to say, "Wow, Mario could have Luigi, Peach, Bowser, Yoshi, Wario, Rosalina...ect ect." "Sonic could have Tails, Knuckles, Eggman ect ect." Or "I want Mega Man EXE and Zero...**** YOU!! The GBA was Great System!! It Had good games!! Should have called it the SNES 2!" And as you said, Metroid and DK had characters that felt like they were missing, in the case of Ridley, K.Rool and I would say Dark Samus and Dixie as well, with the last one still not playable. Or Kirby with B.Dee being in so many recent titles in some capacity.
If this were like FE or FF, where the main cast is constantly changing, this wouldn't be an issue. The newest protag could be in or something. But Zelda changes a lot of it's characters, while Link, Zelda and Ganon are constants or near constants. It makes the rest of them seem not as worthwhile in this particular context.
Like, there's only 2 people who'd like "Demon Train Chancellor Man" from Spirit Tracks for example, and that's being real generous. At least the likes of Midna, Skull Kid, Impa and to a lesser extent Vaati have had solid and consistent support. And even then, there's still 2D era Ganon who could be a cool character to people.