One thing I'd like to add to the whole Xenoblade Chronicles thing is that characters from story heavy games are more difficult to add in advance than a Pokémon since Pokémon characters take a concept, run with it, and finalize it long before the game itself is complete. Characters from story based games change and grow throughout the game and its development, and if a character changes after they've been added to the game, you end up with a character like Roy.
Roy kinda dodged a bullet since his Smash interpretation is more popular it seems, but I can't imagine that working more than once, especially with well liked characters like Noah or Mio.
EDIT: To clarify since I didn't outright state this: The problem with adding a story based character early is that if anything changes the character in Smash won't match up with the character in their home game, potentially to a very strong degree.