I highly doubt they would ever go after a protagonist over a mascot, especially if that mascot is more popular. Besides, Sakurai has no problem adding another swordfighter in Smash. I mean, we have Roy, Cloud and Corrin in the last game as DLC and in Ultimate, we have Chrom. Why not add one more?
Example, Pokemon. Pikachu got in wayyy before Red and Red is the protagonist of the original Red and Blue