The blatant 1 for 1 clones: These are characters that are the closest to another character and have not received any modifications to make them more unique (the case being for Dr. Mario). However, I do see the possibility of Lucina getting de-cloned since at least she is her own separate character and merely a descendant of Marth canonically. As for the rest, I don't see them being as likely unless circumstances go in their favor like they did for three of them in Smash 4.
: Roy has received significant changes in Smash 4 where he has a much more definitive playstyle that he can call his own. As far as representing Fire Emblem, he is the only character that comes from a timeline separate from both Marth and Ike. With these, in my opinion, do not look like points strong enough to make him a guaranteed mainstay compared to the other Fire Emblem veterans.
Lucina?: Like I said earlier, I believe that Lucina can be reworked. She is her own distinct character unlike the other 1 for 1 clones for the most part. Where Dr. Mario is Mario in a doctor's outfit, Young Link is Link's younger self, Pichu is the pre-evolution of Pikachu, and Dark Pit is a literal clone of Pit, Lucina has the most potential to be different. We will have to wait and see if they're willing to change her moveset.
Pokémon: Some may argue that Smash has too many Pokémon. With new games and generations in the series, it's difficult determining which Pokémon are going to be added. So much so that Sakurai had his own seperate criteria for adding them. Popularity is major for them, which will help Charizard, while Greninja represents the Kalos region and is not another Gen 1 Pokémon. Whatever Sakurai/a possible new director will decide on will be the judgement towards each one.
: Toon Link was a character that many believed was at risk. It was surprising when he was announced, and how it was so soon. When Smash 4 came out, we had no new Zelda characters. Just all the ones in Brawl ported over. So in Smash 5, will we see a new Zelda character? And would it still warrant his potential to return? Only time will tell.
Surprise 3rd party characters: By surprise, I mean they're characters you would never expect to be fit for Smash until you see them in action. Unlike Sonic, Mega Man, and Pac-Man, these two tend to stick out like sore thumbs. Snake is from an M rated series that rarely shows up on Nintendo platforms, and was a favor to Hideo Kojima. Ryu was shocking in the sense that he is another Capcom rep, is from a different fighting game franchise, and his recent entry is PS4 exclusive. They seem more like favors to the owners rather than celebrators of Nintendo's history in comparison. There is no certainty with predicting their future relationships.