I think Sakurai has probably gotten an early peek at Fire Emblem, it's always seemed like Intelligent Systems have worked very closely with him when it comes to promoting their new games in Smash all the way back to Roy getting into Melee. We also know that he got an extremely early look at Pokémon X & Y so he could include a newcomer from Gen 6, and a lot of the things about Greninja, like his water swords, was Sakurai's own ideas just based on the design.
I'm not sure it'll be the same with Metroid as it's a series that doesn't have to promote its newest games in the form of characters, and it also seems like in the other cases it's been Intelligent Systems and Game Freak who have taken the initiative and invited Sakurai over. If he were to get a look at Prime 4's concept art then I think he'd have to be the one taking the initiative, and I'm not sure he'd take some of the Prime 4 team's time if he weren't 100% certain that he wanted to include a Metroid newcomer, which I find doubtful as it's not a franchise that's very character-centric. Granted he might have gotten a look in if only to see what their Samus and ZSS designs look like.
As far as Ridley is concerned I don't think it matters much though, if he is in Prime 4 then I doubt they'll scale him down, it's in a 3D environment where I'd most expect his proportions to be ill-suited for Smash, especially as far as his wingspan is concerned. They also already have the Samus-sized rival in Sylux which eliminates any need there might have been to scale Ridley down. Sakurai already knows everything he needs to in regards to Ridley, he's had to hear about that darn dragon for as long as we've voiced our support for him, so Prime 4 would have to do something really special with Ridley if it were to make any difference.
Like you said I think SR will be the Metroid game they take most of their inspiration from, especially if Samus' design changes to her SR suit as her silhouette in the trailer might indicate. I don't think Ridley's design will necessarily follow suit though (whatever his role will be), we know we're getting BotW Link despite Sheik and Ganondorf not having designs from that game, so Sakurai will probably do whatever he wants to.