If it appears in a stage, yes, if it's only available from the music box no. Basically I consider the representation anything you would come across naturally while playing the game, anything you have to search for in the menus is not enough.
Fatal Frame is second party at worst, and first party at best. Unlike others however this was an acquisition, and therefore was Third Party 'till nintendo bought it out when it was about to go bust making Fatal Frame IV. Now Nintendo owns at least the publishing rights to any new titles in series (but not the old ones it seems given Fatal Frame III was recently released on PSN... though it would be lining Nintendo's pockets, so who knows?). Exactly how much they own is not known, and they have yet to develop any of the games, but it is arguably a Nintendo IP.
Magalor:
Chances: 2%
Kirby's pretty much complete, although the final boss true villian style character is the one thing you could argue it's missing. He's the most recent, but that doesn't mean much. Badana Dee has the popularity vote too, not helping him.
Want: 25%
I like me some Kirby Villians.
Fatal Frame Representation:
Ho boy, this is a hard one for a fan to write about. Fatal Frame, or Project Zero as it's known in my country, is rated 18, deals with mature themes (sororicide, torture, insanity, cults), and in my opinion the only actually scary survival horror franchise. The main characters a bit generic, and don't have enough powers to really serve as anything, and the ghosts often have wounds from their deaths and expressions of pain and suffering... not exactly smash friendly when the game doesn't even allow guns. In all likelihood I would imagine most of the series would be unusable as even trophies or stickers...
That said there are 2 reasons I think Nintendo might want to put the series more into the public knowledge:
The Wii U
and The 3DS.
The simple fact is the hardware is perfect for a game where you take photos of ghosts, as is evident by the Spirit Camera game on the 3DS. It was really good (assuming you played it in the dark and had a torch to scan the Diary of Faces AR book), reasonably well recieved ( often very well as an AR game, though often poorly recieved as a new Fatal Frame due to it's short length), and even got a Miiverse page. The fandom is pretty niche, but we're clamoring for more, and most of us want it on the Wii U or more Spirit Camera spin-offs, and with proper advertising the simple fact it utilises the hardware so well could make it quite desirabl, and hopefully quite successful... though if Nintendo will feel this way is questionable, and if they think smash is the way to do it, or if Nintendo Directs are good enough...
So now let's get down to what I think is a reasonable cut-off for significant representation and rate each seperately:
A Playable Character: 0%
It's hard to vote a Nintenod franchise out, but honestly nothing fits. The girls don't have enough for a moveset, or the importance to have one made up, and the ghosts are too creepy to get into the fray... it's a pipe dream at best.
A Stage: 0%
While a stage itself may seem innocuous it's still pretty morbid, and will likely again include ghosts as hazards... not in a game kids will play.
An Item: 3%
The Spirit Camera of the side stories or Camera Obscura of the main series is pretty iconic, and would make a pretty obvious item pick to represent it... for more than say a submarine gun. I would put this higher (probably topping the 10%) if it didn't likely bring with it trophies of the ghosts, and this is the crux you'll find throughout this post.
An Assist Trophy: 0.5%
Ultimately, it'd be one of the girls doing the exact same thing the Camera could in a players hands, and they as characters aren't enough to get people interested, so are unlikely. They may however be easier to balance than the item so may be picked, but I don't think it likely.
Music used in another stage: 10%
And here's where things get interesting. Luigi's Mansion 2 is a stage about haunted houses, and Fatal Frame is a series about Haunted Houses... perfect, no? Certainly more fitting than Tetris, and despite Fatal Frame mostly having ambience created by moaning or shuffling rather than actual tunes there are a few tracks that could work quite well on a stage. I've listed all the tracks I think could work (and are iconic enough to their games) from the 3 games that where made after Niintendo's Aquisition of the title:
It's not a lot given that it's basically everything I could find in 3 games, but you only need one in my books, and they could put a few to sit alongside the other themes. I think one of them being chosen has a pretty decent shot, just not a huge one because there's a lot of competition.
That which does not count includes Tophies, Stickers and Music only available in the Jukebox. Basically if you can't come across it during a normal game I'm not counting it as enough representation for this concept!
So that looks like 13.5%, but it isn't. While the AT and Item are exclusive to each other the music has a notable crossover, I think about a tenth of the music's chance comes bundle with the items so it's more 12.5%... then we get into the legal side of things. While Nintendo kinda owns the series, that's the crux, they've never developed one of the games, and only parcially own it as far as I can tell... that said I have no clue who would own the other part considering it bounces between developers... and given it does whoever it is probably doesn't mind it getting into smash... but second party games come with an inherent risk, and this isn't as big as Fire Emblem or Pokémon so I don't think it can overcome it as easily... so I'm halfing that score.
Chance: 6.25%
Music is it's lifeline really, and even then, it's just not enough to make it likely. Possible, very much so, but not likely.
Want: 95%
Not 100%? Well, Project Zero is creepy, and if thrown in could be too mature for smash, hurting the dynamic (like snake did imho). I do however feel that the small amount that would be represented wouldn't effect it, and trust that Sakurai wouldn't damage the integrity of the series with it, but I can't give 100% because as much as I love Project Zero, and want on the Wii U, I love Smash more.
Sora: 1.2%
I think we're pretty sour to Square, though I think he'll still be higher than Cloud.
Toon Zelda/Tetra: 36.2%
Still Zelda's most likely bet.
Slime*5
(Goo just goo-ldn't write more than Gr-ooze about such a low chance concept goo-ld goo Cheezey? I'm dis-slop-ointed in goo!)
Btw, I find the disparity between the cutesy Kirby visuals and the Fatal Frame title in the OP hilarious.