The thing with the one-off factor is that Sheik got in because Zelda got in, and vice-versa. They were intentionally added s a pair due to a mechanic.
This isn't like other one-off characters and there was no way to know Sheik would not reappear either way. The mechanic came first. Nowadays we have a lot more one-offs that only appear at best via cameos or spin-offs. The only consistent character design is mainly Tingle otherwise(and do note that his cartoony look is pretty much just more colorful). Others still exist like Beedle etc., but they're usually not as major of characters that get recurred. Besides that, Impa suffers from being effectively a fully unique design in multiple games, something Link and Zelda don't have an issue with. Ganondorf barely does either(with only the WW and TOTK versions being noticeably different from OOT and TP respectively). Zelda still has the same core design, with different outfits, in most games too. Sheik aside, of course.
As for Sheik, we don't exactly know if she was planned for TP or if a design was made based upon the TP style. The way Hyrule Historia reads is a bit vague enough to take it either way. Her returning made sense at the time, due to Brawl keeping the same transformation mechanic. It's also way less work than doing an entirely new character. Besides that, he had planned at one point(enough to put files in) for a Toon Sheik. And contrary to many theories, this would've said Tetra if that was the original plan. He wouldn't use such a clearly specific name otherwise. There could've been various kinds of code names it could have, but that's not the case here. So even being a one-off, he had thought about a clone of her, being a full Smash OC in the same way that Giga Bowser actually is(Mr. Game & Watch is borderline, since it's a fusion of all his games into one moveset. There is no actual Mr. Game & Watch in his games. He's only technically a Smash OC, but Giga Bowser was straight out made for Smash as a design, no different from Master Hand or Crazy Hand, etc).
More to the point, being a one-off isn't a detriment on its own. It's just that Smash represents the most important characters in Zelda, with at worst regular Ganon not appearing outside of a cameo or mention at first. He has zero references in Melee, and is mentioned in Link's Smash 64 profile. In Brawl, he appears in his TP design, and Ultimate changes him to the OOT design. Puppet Ganon is also never a Sticker or Trophy oddly enough. ALTTP Ganon isn't given any love either. Thankfully we still get a pretty strong usage of him via the Final Smash and related materials, as well as a Boss eventually. Sure, it isn't his most memorable design(ALTTP), and functions very differently from him in terms of abilities, but it's still there.
I could absolutely see other notable ones getting in regardless. But as noted, it's an uphill battle. With no specific character being rallied behind, it leaves a ton of fan favorites who get put in other roles since they still get represented, to please as many at once. Incidentally, Impa took a lonnnnnng time to appear, whereas Tingle was there by Melee in some way. It's unclear why. Maybe he was more popular in general? Who knows. Impa didn't exactly become notable till OOT where she played a role besides sending you on a mission(or have any in-game appearances besides the CD-i games).