Alright, so for context these were my Melee clones: Donkey Kong Jr, Young Link, Pichu, Black Shadow, Poo, and Glass Joe. I actually added Falco in Smash 64, so that's why he came back earlier on and why he's ineligible for this round.
A few of these characters have sufficient replacements. DK Jr and Poo feel like they're rendered a bit redundant with Diddy Kong and Lucas being added. Diddy and Jr play pretty different, but he's completely replaced him in the DK franchise and Mario spinoffs by now as well. Glass Joe is someone I'd love to keep around as a staple, but with his more defined joke character role and the fact that Punch-Out is largely dormant it makes sense to let him go for now. Young Link was in consideration, but I dunno. I just thought the other options were more interesting, and the Zelda releases we did see after Melee aren't really concerned with him.
Black Shadow is salvaged, because I like keeping more villains around and frankly it doesn't make a lot of sense to scale F-Zero down. Between Melee and Brawl it pretty much doubled its number of games with three new entries. Black Shadow had a prominent role in GX and seeing how popular Ganondorf is to play, I imagine Black Shadow would end up with a fairly similar legacy as a big dumb bruiser. With Falcon acting as something of a Smash mascot himself I think it's nice for him to continue to have a foil, B.Shadow is like his Akuma.
Pichu gets to stay and receives a rework comparable to his buffs in Ultimate. It, like Glass Joe, kind of debuted as a joke character. But Pichu is an easier concept to refine, making it a full on glass cannon and maintaining its slippery speed and size. Worth noting there were quite a few new baby Pokemon in Gen 4, so Pichu actually kinda makes sense even in the context of the way the Pokemon series is progressing.