I would say that Shantae's somewhat iconic for her obscurity, like Ness, but I constantly remember how well the Kickstarter did (despite being blindsided by Mighty No. 9, with Shantae having the last laugh).
The main problem, if indies are the case, is that Shantae and Wayforward constantly gets the short end of the stick. With Shantae being the oldest indie icon (heck, she was conceptualized before Cave Story started development), with Nintendo loving to constantly bring back old faces, Shantae, unfortunately, doesn't really get that much love from them. She had to piggyback on the magazine that wasn't even attached to Nintendo anymore, got a few ads on the eshop, and a cameo in WarioWare DIY, which did just about nothing.
In terms of Indies, the main reason Shantae and Shovel Knight are butting heads in the ballot is for one reason: Nintendo's pushing Shovel Knight a lot more, while Shantae is the one truly supported by a fandom (and Wayforward's encouragement).
Considering how Wayforward has said that they loved working on Nintendo platforms, with Matt Bozon considering the Nintendo fans their best audience, they don't really get much out of it, which is most likely why Shantae's been appearing on other platforms.
It's like Shantae's the older sister who gets nothing for mowing the lawn, cleaning the patio, and taking out the trash, with Shovel Knight being the younger brother who gets $10 for washing the dishes and existing.