That's a strange thing to gauge. I mean poll results speak for themselves. As far as I can tell, SK is the indie char most talked about, most recognized, the one with the most hype.
I MEAN... he's the one that got an Amiibo.
And besides Shantae, I recognize none of the others on name alone.
That may out me as a filthy casual, but I think the popularity or at least notoriety of SK is important.
It does basically make him the face of indies
A big difference here is that Quote and Reimu originate from Japan. We know that Sakurai prefers characters originating from Japan (only 3 characters on the roster originate from locations outside of Japan, being Diddy Kong and now King K. Rool and Dark Samus) (see also, the criteria for third parties having to be from "globally-recognized series
from Japan"), and the western indie genre is too new and still needs to properly establish itself. Shovel Knight was the only
western indie character with a chance, and we know how that went. So, let's look for
Japanese indie characters that have seniority/have established themselves. There are really only two, being Quote and Reimu.
Cave Story has been around for over a decade (2004), and has been on every Nintendo console since the Wii/DSi (Wii U through the Wii Shop Channel). It's the epitome of indie success, with the whole thing (coding, art, music, etc.) being developed by one person. The game has received mass acclaim since it's release, and Quote has appeared in a fair share of western indie crossovers if that means anything.
Touhou as a series has been around for over 20 years (1996), and Reimu is the main character of the series. Touhou is a genre in of itself, being known as the originator of the bullet hell genre. Touhou is also
huge in Japan, having it's own section dedicated to it during Comiket, the largest Japanese fan-event in the nation. I think we're seriously sleeping on Reimu, as much of a meme as she was.
Even Shantae, while originating from America, has seniority, being on Nintendo systems since the Game Boy Color, giving her a chance, if not a smaller one. Maybe DLC.