After all that's happened, I'm predicting Doomguy and Ryu Hayabusa as the next two characters, or at least someone from those companies.
Of course you have that comment of Bethesda talking to Nintendo with regards to Smash which could mean nothing, but after these last two reveals especially, I think the DLC might be from companies that have done some major collaboration with Nintendo in terms of the Switch, or at least companies Nintendo wants better relations with. Atlus is working on SMT 5, one of the major announcements from the first Nintendo Switch conference, is working on P5S, but has recently had more of an emphasis on Sony. Joker could very well be a way to maintain a strong working relation with Atlus, especially since Persona 5 was such a breakout success that it proves Atlus is a big player.
Square has shown support for the Switch from the very start with DQ11, but that support has only continued since. From porting over multiple previously exclusive Final Fantasy games, to Romancing Saga, to Seiken Densetsu, Square has been one of the biggest third party collaborators with Nintendo. They've had big sections dedicated to them in several directs. It's clear that Nintendo views Square as an important third party, and adding in Hero to Smash just maintains that relationship.
Microsoft and Nintendo's recent collaboration is well-documented, but of course with Minecraft on the Switch, that Xbox live business, Microsoft approaching Nintendo to put Cuphead on the Switch, and that rumour of Ori and the Master Chief Collection coming to Switch - yeah, it seems like Microsoft and Nintendo aren't as direct competitors anymore. Microsoft is obviously one of the biggest companies in the world witha huge influence in the gaming sphere as manufacturer, developer and publisher: having them remain collaborate rather than competitor is very valuable to Nintendo I'd imagine.
As for my predictions, Bethesda is undeniably one of the biggest third parties actively supporting the Switch, and perhaps the biggest western third party in that regard. To me it says a lot that they:
-Advertised Skyrim in the reveal of the Switch
-Had Todd Howard appear in the initial Switch conference
-Included their own IP as a part of Skyrim (albeit as of late this has become a lot more common)
-Went to the effort of porting not only Doom, but Wolfenstein
-Ported Fallout Shelter
-Are advertising the Switch as one of the primary ways to play Doom Eternal at launch
From my perspective, this signifies that Nintendo wants to keep Bethesda as a primary associate, and adding a Bethesda character to Smash would serve to only enhance that. It's not that far-fetched, especially when observing the amount of Square games on the Switch after Cloud got in. Now, why Doomguy over The Last Dragonborn? After all, Skyrim was one of the most heavily advertised titles for the Switch and is incredibly iconic and influential. Admittedly, I'm likely biased to an extent, but I feel like Doomguy would be chosen for similar reasons as Banjo over say, Steve or Master Chief. Doom's legacy is essentially universally known, but Doom itself has had a surprisingly extensive history with Nintendo. The original Doom was ported to the SNES, an entire new, original Doom game was created for the N64, both Doom and Doom II were ported to the GBA, and of course there's the rebooted Doom games. That makes Doom 3 the only mainline Doom game not on a Nintendo console, but Doom 64 is entirely exclusive and is acknowledged as a primary Doom game. Hell, before even Commander Keen and being known as ID, Carmack and the crew proposed a PC port of Super Mario Bros 3 to Nintendo before bieng turned down. That, combined iwth some interesting comments by the Doom staff such as Mick Gordon working on a Doom-related project and Bethesda saying Nintendo fans are in for a Doom-related surprise, makes me lean towards Doomguy as a potential Bethesda character. I do concede it could very well be Dragonborn or perhaps even Vault Boy instead though.
Finally on to Ryu Hayabusa. From as far back as 2014, Koei Tecmo has had some major collaborations with Nintendo. Hyrule Warriors comes to mind as one of the first times in recent memory Nintendo has lent off one of their entire first-party IPs to a different studio for a big release, Zelda at that. Hyrule Warriors seemed to be a success, because this active partnership later continued with Fire Emblem Warriors. That game was also one of the primary announcements at the first Switch press conference. From there, Koei Tecmo has only gone farther, bringing over multiple Warriors games, countless Atelier games under Gust, many smaller projects, and even Dead Or Alive Xtreme 3, not to mention their work on P5S. Koei Tecmo is clearly one of Nintendo's primary active associates alongside companies such as Ubisoft. As for Ryu himself, I see him as one of the big remaining NES icons not yet in Smash. Ninja Gaiden has a storied legacy from the NES to the modern-age reboots, with both styles having great influence over action games. One could argue the original Ninja Gaiden games essentially popularised cutscenes and in-depth story-telling in video games. Ryu has essentially become the mascot of Koei Tecmo, even becoming an important character in other franchises such as Dead or Alive and making appearances in Warrior games. This could also be Kasumi from DOA instead, as she too is one of KT's most popular characters, but her lack of general legacy on Nintendo and the fact that Ryu has essentially become one of the faces of DOA as well makes me question her.
Admittedly, I'm a bit more uncertain on a Koei Tecmo character compared to Bethesda. That's not even mentioning other potential companies, such as SNK and Terry Bogards, or Ubisoft and Ezio. Truth is these last two characters really could be anyone.
But that's just what I think.