I think the biggest challenge facing Indies is that they tend to be a little transient in terms of their relevancy and popularity, which is a big problem for a third party.
Third parties tend to be long-established names that have endured in the public consciousness for about 2 decades prior to being added. If you can only have a dozen or so characters from across the entirety of gaming that isn't Nintendo, you may as well make sure it's a character has proven to be remembered and influential.

,

, and

are the exceptions, but Bayo is a honourary Nintendo franchise, Joker is the lead of the most popular entry from a 28 year-old series, and Minecraft is so massive that it already has a lot of legacy.
In contrast, Indie character tend to be one-offs rather than being from massive franchises, which causes them to kind of come and go. Super Meat Boy and Castle Crashers used to be the face of Indie games, but they're not nearly as popular as they are now.
You can even see this in Smash, to an extent. Sakurai made a big deal in one of his PotDs about an Indie character getting a trophy in Smash. That character was Bit.trip Runner, which isn't actually what would excite audiences in 2025 and beyond.
Shantae and Sans seem to be in the best spot in this regard, as Shantae has been receiving new entries for about 15 years now and Undertale is still remembered fondly 10 years after being released. However, even they aren't as massive as they were in the late 2010s, with games like Balatro and Hades now being seen as the face of Indie gaming.