Okay, IF Ridley is a boss, he will surely be a boss in both versions. So what stage could be big enough to handle a fight against a big boss like Ridley in the 3DS version? The stage have to be based on a handheld game, obviously and also game in which Ridley appears, so the only options are Fusion and Zero Mission. The locations where you fight Ridley in these games are small and claustrophobic, I don't think they will be suitable for Smash Bros. So, where exactly would we fight him?
I still don't think he is a boss.
Because he isn't? The fights against Yellow Devil are harsh indeed, but it still is just a regular boss. If you want compare Ridley to a Mega Man villain, you should be comparing him to characters like Dr. Wily, Sigma, Copy X, etc. Ridley is not a simply boss in Metroid games, he is Samus Aran's arch-enemy.