If third party support is how this is being measured, might as well boot Mega Man too. While Capcom's Wii U support is better than Konami's, it's still pretty weak. Both companies' output on 3DS is fairly decent. Sonic is the only character that truly belongs if we're going this way.
Instead, I prefer to view a third party character's inclusion based on what the character means in relation to Nintendo's history. That means Snake would likely still be out having only appeared in a single, completely original exclusive (albeit non-canon) game, but Mega Man definitely has a place. Additionally, Sonic absolutely belongs in terms of Sega's rivalry and subsequent partnerships with Nintendo. If any Konami character deserved a spot, a representative from Castlevania makes the most sense.