The thing is, Lucina would still be fine with me if reduced to an alt. Not that that's a realistic thing unless Sakurai no longer is making the next game. She didn't gain any new techniques at all that makes her feel unique enough. Dark Pit has actual different moves, and so does Dr. Mario. They make far less sense to be alts.
But yes, I do agree that Roy and Lucina are the most likely cuts. Also, I feel like Ike is the Lucario of Fire Emblem. Immensely popular, not the "main" character of the series as a whole, starred in a major media item(Ike in his two games, and Lucario in the movie), effectively a poster boy lately for a lot of stuff... but to be fair, it isn't a perfect comparison, and I'm not talking about their abilities. XD
It'll be interesting what new characters are announced for the next overall Smash game(the real Smash 5, as in not a Smash 4 port/improved port for the NX).