The Echidna Clan was a plot point in the Sonic Adventure game, before any of the Archie comics delved deep into their lore. Since the movie goes by it's own canon also, I think that's why despite the Ken Penders situation, they were still used
Perhaps we could see similar things happen with other content not exclusive to Ken penders, but tied to him nonetheless, like the Black Arms (Though that's if they want to keep that for Shadow in the movie Canon)
Whether its Eggman, Arle, or some other dark horse, I will say Sega's got a decent shot at having someone. They've had characters in the two previous DLC cycles, and given that Square and Microsoft have doubled dipped in terms of Fighter's Pass, a company like Sega that has arguably an even more consistent relationship with Nintendo feels like an easy source to pull fighters from yet again.
If it's something Sonic related, here's something I'll say
The content that Square and Microsoft got in Both Fighter Passes had no presence in Smash before. Dragon Quest, Banjo & Kazooie, and Minecraft were completely new, and the new FF7 Content we got in FP2 with Sephiroth and all the spirits, costumes, music, stage, were all new to the game, otherwise everything else in base game was just leftovers from Cloud's Smash 4 DLC. This also extends to Sega regarding Persona
Regarding Sega, if It's something Sonic related, since the other Sonic characters have had a presence in the game since Sonic's introduction into Brawl, I could see a case where regarding negotiations, they probably negotiate everything during the base game, Including the Assist trophies, spirits, maybe even the Costumes (though I'm not sure on that). the other Franchises mentioned were probably in talks for a good while, but their first negotiations were during when DLC was decided to be a thing
If another Sonic character was decided to be a thing, then this would be the 2nd round of negotiations they will go through. I will say this is probably something that Bomberman had to go through to get his Deluxe Mii Costume, and it could extend to a Full fleged fighter in the case of Sonic.
The reason I even mention all of this is because (and this is not because of your comment, but other comments I've seen in the past), It would be weird that Another Sonic character isn't in the same priority of Steve and Sephiroth if Sakurai's Comments about "1 or 2 Extra fighters" has any bearing, and couple with the Sonic costumes appearing in Joker's pack, I have seen these as reason against another Sonic character
But I think in regards to Sonic, Unlike Steve and Sephiroth, The other characters do already have presence in the game and have had presence since Brawl, so if a FP2 was deemed as a risky avenue to go into, It's not like there would be a waste of talks in regards to Another Sonic character, unlike with Steve, Sephiroth, and etc