Speculation at this point is really just a matter of how you interpret Sakurai's 'hope you aren't expecting too many newcomers' line. Are we just getting fewer unique newcomers this time around, with Echoes bringing it up to about as many or even more total newcomers than usual? Do the two categories together still add up to noticeably less than usual? Is he just drumming up hype by lowering expectations? Rather than try to pin down a definite roster due to the many ways this could be interpreted, I'll just go over anybody I think has a notable chance.
Unique Newcomers (First Party)
Paper Mario - A pretty popular pick for a new Mario character, and pretty much the frontrunner with Waluigi and (Captain) Toad out of the race. Popularity and relevance are both there, and he even already has a homestage, but he would 100% HAVE to be a unique newcomer, and much bigger characters would likely be a priority. Not likely, but a decent chance.
Skull Kid - With every other pick trapped in a snowglobe, and Majora's Mask repped by a new Assist Trophy, and his own still missing after the second wave of disconfirmations, Skull Kid feels more and more likely, especially with his known popularity, and his relevance thanks to the Majora's Mask 3D release close to the project plan finalization. Actually pretty likely.
Bandana Dee - As much as I support and believe in Bandana Dee, I feel it's necessary to avoid a tunnel vision mindset and actually look at how popular he was at the time of the project plan. Even though he's EVERYWHERE now, he hadn't had an exceptional amount of appearances by late 2015, so I feel like in a similar situation to Ashley, he's nowhere near as likely as we actually think. Regardless, Japan did still like him a lot at the time of the ballot, so we'll just have to see. 50/50 split on his chances.
Pokemon - Jeez, this is practically impossible to choose. Setting aside the validity of any 'leaks', although Smash tends to push a Pokemon from the newest generation, making Decidueye, Incineraor, or Buzzwole feel likely, this is simultaneously the Smash focused the most on delivering on fan desires, making Gengar, Sceptile, and Gardevoir feel just as relevant and possible. Christ, Pokemon honestly has way too many characters legitimately in the running to pick one, but one is practically guaranteed. (Zeraora more than likely isn't happening though)
Elma - Big question marks everywhere. I feel like they'd prefer to hold off on Xenoblade X representation and instead go for the more tantalizing Xenoblade 2 promotion later down the line. Additionally, Elma wasn't really all that popular as a pick until after the ballot, missing out on the biggest proving ground for popularity available before the project plan finalization. She honestly doesn't feel that likely, sadly.
Isaac - It feels bizarre to say this, but Isaac feels genuinely likely at this point. Between Ridley and K. Rool, we've somehow arrived in a timeline where Sakurai heeds the longest-running fan requests, and Isaac is certainly extremely high among fan desires. As proven by K. Rool, relevancy be damned. By sheer force of popularity and demand alone, Isaac feels pretty gosh darn likely. And that still feels weird to say.
Rhythm Heaven - WIth Chrom making the leap to playability, and Rhythm Heaven having been in some capacity developed for Smash 4, we're more than likely seeing the series turn up in some playable capacity. Similar to Pokemon, there's a bunch of characters to choose from, so take your pick- Chorus Kids, Karate Joe, Tibby, what have you, the series feels very likely to get a rep in the game.
Unique Newcomers (Third Party)
Lloyd Irving AND/OR Heihachi - Bamco's inclusion, Mii costumes, yadda yadda for both. Sakurai interview for Heihachi. Long-term notable popularity for Lloyd / Tales in general. One or the other feels pretty likely.
Geno - BREAK THE LIMITS, SAKURAI! CONFIRM THE FINAL MEMBER OF THE HOLY TRINITY OF SMASH SPECULATION!... Eh hem. Pretty likely.
Crash Bandicoot - Crash has had a strong presence as a desired 3rd-party for quite some time, and while his big jump to the Switch may have come a bit late to count for his chances here, I don't doubt Sakurai's ability to pull in whatever he wants to satisfy fans. The timing feels a bit off though, so I'd give him an unlikely for base game, but 50/50 for DLC.
Banjo-Kazooie - Similarly to Geno, BK has been planned by Sakurai himself in the past, as far back as Melee. With fan-demands in mind and Microsoft being open to the possibility, the bear and bird have a definite boost in possibility, but I wouldn't get my confidence too high up. 50/50 split
Echoes
Ninten - Incredibly easy to add, given his likely total resemblance to Ness, and quickly rounds out the trio of Mother protagonists. Populariry may be a bit lacking, but the desire to have all three Mothers represented exists. 50/50 split.
Black Shadow - Fan demand, push for more villains, keeps Falcondorf intact for losers like me who miss lagless Up Smash. 50/50 split.
Impa - Impa is the last remaining major character of the franchise to not show up in Smash, and her Skyward Sword design would work extremely well to utilize Sheik's moveset. Even better, Impa has had a definite popularity over the years. Likely.
Dixie Kong - As proven by Chrom, an Echo doesn't have to only take moves from the fighter they're based on- using Diddy as a base, but giving her a smaller version of DK's Up B (and even possibly Down B) utilizing her hair is entirely within the realm of possibility now. While K. Rool answers the cries of DK representation, Dixie on her own still holds a massive amount of popularity. Likely.
Shadow the Hedgehog - In a similar case to Chrom and possibly Dixie, Shadow can escape the cries of 'TWO Spindashes and a Spring', most likely with the utilization of a Teleport for Up Special, and as one clever user somewhere mentioned, a move similar to Dark Pit's arrow for Chaos Spear. However he's done, with Richter breaking down the conception of 3rd-party Echoes being unlikely, he's practically a guarantee at this point.
Isabelle - New face of Animal Crossing and a beloved character, but falls into the Animal Crossing trap of not being much of a fighter and not having much to pull on. By far the easiest method to remedy this is to have her as an Echo, and the only way I see her entering the fray. The Echoes we have so far proove a lot more effort is being put into them than we thought, and her animations can definitely be changed to reflect her personality. Likely.
Medusa - Once again, Echoes can defnitely have more effort in them than we thought, and with some tweaks to effect coloration, many of Palutena's moves fit Medusa perfectly- and again, the focus on villains seems notable, so a villain from Sakurai's adopted child seems fair. (And it means we can get Hades as a stage boss, which would make me BEYOND ROCK-HARD). On the other hand, her popularity is a bit lacking. 50/50 split.
Ken - 3rdpartyechoes.exe, orginalEchoFighter.jpg. Likely.
If you held me at gunpoint and I had to take a shot in the dark what the last few newcomers and echoes we would see are, I'd say-
Skull Kid
Pokemon
Isaac
Rhythm Heaven
Lloyd OR Heihachi
Geno
Impa
Dixie Kong
Shadow
Isabelle
Ken
(With HOPEFULLY Bandana Dee and Banjo-Kazooie making the cut)
EDIT: I would love to be surprised and see characters I didn't find as likely, and especially ones I didn't even mention.