I don't know why people think second-parties aren't more unlikely to be included because they are second party. Sakurai goes to the effort to get third-parties, characters not even partially owned by Nintendo, he's gotten rights to most of the popular 2nd parties last time around (they just weren't playable - other than Pokemon), and there already are second-parties on the roster. Yeah, Nintendo does own a majority of Pokemon, but Sakurai still has to work with Game Freak like he would any other second-party. It's possible we don't get any new ones this time around just because none have extremely good chances, but assuming being 2nd party majorly hinders chances is simply an unfounded theory.
The Bayonetta IP isn't owned by Nintendo, they just own the rights to Bayonetta 2. Like Pokemon or GS, Nintendo owns part of W101, making them a 2nd party IP while Bayonetta is still 3rd.Similar to Bayonetta being partially owned by SEGA, The Wonderful 101 is shared between Nintendo and Platinum Games.