I think it's more to do with people voting for the character that has a better chance of joining the roster. If Rare went third party completely instead of being owned by Microsoft then you can bet people would be voting in droves for Banjo. Instead he's owned by MS and Shantae isn't which gives her a very minuscule edge over Banjo.
I don't think the Smash roster should add indies yet. They're ultimately still third parties and with some notable absentees (
, Simon Belmont, Rayman and Black Mage to name a few) I'm against indie characters for now as they'd look really out of place next to legends like
etc. It's why I find Shantae to be a very overrated character for Smash 4.
I've never understood the hype between neither Shovel Knight or Shantae. I bet if Wayforward or YachtClub Games haven't said anything about wanting them in Smash these two would've gotten very low ballot support. I too don't think any Indies are ready to hang with the big dogs neither, especially since there are other third parties that can match up to the ones that are in the game or have been apart of the franchise. If anything they'll go to third parties that people have been asking for since Melee and Brawl, and will try to get licensing to them. Third parties are suppose to be special. I don't even think it matters how loyal they've been to Nintendo, cause even they kind of forget after a while that they exist up until a new game gets released and then forget about them again. If either Shovel Knight or Shantae got accepted as DLC they would feel so random and somewhat forced.