I don't think you realize just how badly Captain Rainbow sold in Japan. It couldn't sell 7,000 units in it's launch week, and VGCHARTZ has it at just over 10,000 total. You might doubt VGCHARTZ, but the launch week numbers are from Media Create so you should believe those, and since most Japanese games sell half or more of their overall total in their first week, I don't doubt it.
Now Earthbound, which was considered a flop in the West, still sold over 140,000 units IN NORTH AMERICA. Mother 3 was the sequel to a game with an international release that already had representation in Smash, it also pushed almost half a million unites in Japan. Fire Emblem was a long running series when it got it's characters in Smash, and it's over all sales were always decent.
Captain Rainbow is not in the same league as these other franchises. The game reviewed well and has a bit of a cult following, and it is also "Smash Famous" because it's a new Nintendo IP. It is completely possible that the Captain can be a character in Smash, but he is certainly no Marth or Lucas.