Like that idea, so far I though on some characters that could get introduced earlier, so far I though on this, not sure what you think:
Smash 64:
Peach
Zelda
Bowser
Honestly not sure if SSB64 should have any more characters from existing series. However, it might be possible to bring Marth in earlier, possibly replacing Jigglypuff.
Smash Bros Melee (Likely doesnt has Dr. Mario or Young Link, these rather being alternate costumes):
Toad
Wouldn't have enough content for a full moveset until Captain Toad comes out, unless there's a game starring Toad earlier.
Acceptable.
Acceptable if and only if The Mysterious Murasame Castle comes over to the West.
Maybe as a replacement for Falco (Fox, Falco and Wolf are all rather similar).
Meta Knight
Lucas
Diddy Kong
Acceptable.
Smash Bros Brawl:
Mega Man
Pac Man
Mega Man is fine. Pac Man is IMO poorly suited for Smash, so unless there's a game ITTL to buff out his moveset without resorting to other Namco titles he should be scrapped.
Probably not both at the same time: their movesets would mostly involve similar content from the Mario spinoff games. Also, you stated Wapeach would debut in Mario Tennis 64 instead of Daisy taking her place, so Daisy would be even worse suited than Waluigi ITTL unless Daisy gets her own game.
Unsure, although given modern Sonic is a lot better off TTL it could work.
Probably workable.
Smash Bros 4:
Simon Belmont
Dr. Eggman
Acceptable, although see above regarding Eggman.
Not sure.
Assuming Rare's relationship with Nintendo is a lot better, I could see Banjo-Kazooie in Smash as early as Melee.
Not sure.
Acceptable.
Petey Piranha (gets upgraded from boss to playable)
Porky Minch (same than Petey)
Ridley (same than the previous ones)
Ridley is okay. Petey Piranha and Porky Minch would be best to stay as bosses. If you do want another representative from the Mother series, consider Ninten from the original Mother.
Geno (Likely as DLC but fully in game on the next one)
If Super Mario RPG spawns direct sequels (instead of giving way to Paper Mario and Mario & Luigi as OTL), then Geno could get in even earlier. Otherwise, he'll never make it.
This would require Square Enix's relationship with Nintendo to be better, though.
Smash Bros Ultimate:
Pauline
Depends on how much of a moveset she has; given your complete retconning of Donkey Kong, I don't think she has much of a chance.
King Boo
Captain Syrup
Gruntilda
Captain Syrup could work; the other two would best stay bosses.
Terry Bogard (As in base game instead of DLC)
Kazuya Miishima (As in base game instead of DLC)
Plausible, although they aren't the best picks for each series. I'd have chosen Mai Shiranui (censored appropriately) and Heihachi, respectively.
Sepphiroth (As fully in game instead of DLC)
See Geno regarding Square Enix' relationship with Nintendo.
Not sure.
See Geno.
Other suggestions I'd make would be replacing Roy with Sigurd (FE6, where Roy debuted, was still in development when Melee released; Sigurd from FE4 would be a safer pick), and delaying Corrin to SSBU for similar reasons.