The difference is one is changing a character to fit a role (boss, clone, and amalgamation - even though G&W did exist prior to Melee, just not the Mr. G&W identity) and one is arbitrarily shoving a character into a series they've never been in for the sake of a second rep. If Sakurai wanted to include Waluigi, he'd include him under Mario, what logic would there be in putting him under Wario, he's never been in a Wario game? If it didn't matter to Sakurai, he wouldn't have categorized him under Mario in Brawl, and there's really nothing since then that would seemingly make him change his mind.
What logic would there be in putting him under Wario?
I don't know, probably the fact that Waluigi is typically
associated with Wario?
Bear in mind, that I didn't say in terms of arbitrarily shoving Waluigi as a Wario character for the sole purpose of giving the franchise another character. If it were all about giving the series another character, then arbitrarily shoving in someone like Captain Syrup, Mona, Jimmy T., Ashley, or even Shake King would be the way to go.
It's for keeping Waluigi with Wario for the sake of
keeping Waluigi with Wario. Other than the whole "he isn't part of Wario's games" excuse, what logic is there to keep Mario, Luigi, and Waluigi all tied together while Wario is not even associated with any of them? It would make
more sense to have Waluigi with Wario, even if it has to break "canon".
We've already got a case where the two are connected in Smash when they "shouldn't" be; the Waluigi Pinball music in Brawl. It contains a sample of Wario's victory theme within it. Said victory theme is from later released game Wario Land: Shake It!, in which Waluigi was not present, and was used for the victory theme for the WarioWare franchise in Brawl, a series Waluigi is
also not present in.
He's made odd decisions before, but there's very little reasoning behind thinking he'd do this. Because he's made unpredictable, strange choices before? Not this kind of choice, and really that's just an excuse for people to justify things that normally would have no weight behind them. "Well it could happen, Sakurai is unpredictable." Sure it could happen... but it almost definitely won't. Sakurai doesn't seem to care that much about series equality to misrepresent the series and include a character that never actually appeared in said series (your examples are just different versions of a character already in their series).
Giga Bowser is a "Smash Bros." character. Not a "Mario" character. So no, there's an example of a different version of a character
not within their series.
And as I said, Mr. Game & Watch
never existed prior to Melee. So that's another case that isn't "just different version of a character already in their series".
The only example I gave that fits is Toon Sheik. And last I checked, 1 out of 3 is not a majority. :/
I also never brought up series equality, so at that point, you're arguing a strawman. And if you think in terms of putting the Wa Bros. together, that actually holds more weight than you realize.
Not to say he wouldn't include Waluigi at all, just until he makes an overdue appearance in a Wario game, he'd be a Mario character.
At this point, making definitive statements such as this is honestly laughable. We really don't know for sure; all we can go by is possibility for either case. I'm not saying it
will happen to where Waluigi is added to be part of Wario's crew in Smash. All I'm saying is that it's possible and reasonable despite being a bit of a head-scratcher.
Especially if you consider that Nintendo R&D1 hates using characters they didn't create (which is part of the reason Wario was created in the first place, to be a parody of Mario to express that hatred), making an actual appearance in Wario games by Waluigi to be a pipe dream, as sad as it is.
Maybe I missed something in the last few pages, but how is Jigglypuff low priority?
I keep explaining this.
Jigglypuff was towards the end of character data after R.O.B. along with other veterans Mewtwo, Roy, and Dr. Mario, as well as Newcomers Toon Link, Wolf, Toon Zelda/"Toon Sheik", and theoretically, "pra_mai". If she was not low priority, she would be inbetween Ness and Bowser in the data instead.
This meant that she was among the expendable characters if time would not allow for everyone planned.
And no, being "easy to make" is not an excuse. Mr. Game & Watch was pretty much the easiest character to make in the series, and he was still among the higher-priority veterans rather than with Jigglypuff and co.
The Starfox character designs are all based on their Command style with a few differences, mostly in wolf's case, and making Waluigi wouldn't fit because, as you said, he's never been in a Wario game before unlike the characters you mentioned who have all, technically, been in their respected games. Overall, I'm just saying if Waluigi WAS in, he'd be counted as a Mario character.
Other than face structure, the SF characters are pretty much original design. There's more differences than similarities to Command style.
And that doesn't change my example of Pit, who was given a completely different design to what he had before for the sake of "modernization" (and no, Uprising wasn't even considered at that point). In a semi-related example, he was also given a style not seen within his series, having a new bow that could be used as a dual-sided blade that splits into two.