Out of this list, I'd probably go with Koei Tecmo with Ryu, Level-5 with Layton/Jibanyan and Grasshopper Manufacture with Travis.
I'm not too familiar with the others so I can't say as much about them, though I suppose I could probably see Taito, Marvelous, NIS, Arc system Works and Spike Chunsoft having potential, though mostly because I've seen their franchises around a number of times.
The biggest third-party developers are already represented in Smash; almost everyone missing is relatively low-profile. That's not to say they don't necessarily deserve a place in the game.
As for third-party companies that are already represented, which characters would they choose if they were tapped for more?
SEGA
Their most requested missing character is Arle from Puyo Puyo, who has decades of legacy and Japanese popularity to spare. If not her, it may be someone from Phantasy Star Online (to promote the upcoming Western release of PSO2), Kiryu from Yakuza (if Sakurai asked for him specifically), or even another Sonic character (considering that it's their biggest franchise globally).
Capcom
Resident Evil and Monster Hunter are two massive and requested franchises. Leon and/or Jill from RE is a no-brainer to me. The presence of Rathalos in the base game suggests that Sakurai considered implementing a Monster Hunter character and either decided against it or failed. However, the Monster Hunter is highly-requested in Japan, so it may still happen.
Beyond those two, Capcom has a wealth of second-rung franchises to tap into. If they got to put two additional newcomers in, I think we might get Dante (Devil May Cry), Phoenix (Ace Attorney), or even Amaterasu (Okami).
Bandai-Namco
Bamco has a lot of roughly equally likely choices. Tekken is a worldwide phenomenon, but apparently Sakurai already tried to implement Heihachi into Smash 4 and failed. Tekken also competes with Tales (Lloyd/Yuri), Dark Souls (Chosen Undead), and SoulCalibur (Sophitia/Nightmare). I can see any of these making it in.
Beyond those, Bamco has a wealth of less-considered choices: The Prince (Katamari), Valkyrie (Valkyrie Densetsu), Taizo Hori/Mr. Driller (Dig-Dug/Mr. Driller), Gil (The Tower of Druaga), KOS-MOS (Xenosaga), Don (Taiko Drum Master), or even Agumon (Digimon). But I don't see any of these realistically happening.
Konami
Konami is a bit of a question mark because as a company that no longer develops video games, I don't know if they're willing to lend more IP to Nintendo for Smash Bros. However if they did, the most likely choices would be Bill / Lance (Contra) by far due to their legacy and status as NES icons. If they wanted to represent Hudson's IPs, they could push for Yugo (Bloody Roar), though that series has been dormant for a while.
Less-likely choices include someone from Gradius/Parodius, some kind of DDR/Beatmania rep, Django from Boktai, TwinBee, or even one of the girls from Tokimeki Memorial as a strictly-for-Japan pick. But those seem too esoteric for Nintendo to bother with at this point.
Square Enix
With a Final Fantasy and Dragon Quest representative already in the game, fans are only really clamoring for Sora (Kingdom Hearts). Whether he gets in is a matter of negotiation with the notoriously draconian Disney. If it falls through, there's another strong option: Lara Croft (Tomb Raider).
Dark horse picks for Square would include 2B (NieR) or Taito's Bub & Bob (Bubble Bobble). If Sakurai specifically requested it, they might give up Crono (Chrono Trigger), but frankly I doubt it.
SNK
I honestly don't see SNK getting a second guest character, but if it did happen, Marco/Fio (Metal Slug) seem like the clearest choice, considering the biggest KOF characters (plus Nakoruru from Samurai Shodown) were "soft deconfirmed" in Terry's trailer.