The way I see it there's two routes they can go about it. This depends on how much they decide to capitalize on the fact that the Echidna tribe was very likely a serendipitous Tyson Hesse change, but Sonic's "power" in the movie is very clearly Chaos power, and in Sonic Adventure it's the pursuit of that power which caused the Echidnas go extinct. Since the Sonic movie has a notable time skip between Sonic as a kid and Sonic as a teen, I'm thinking it's possible that the Echidnas could've gone extinct in that time frame after obtaining the Chaos Emeralds, with Knuckles being the last of his kind. The second movie could verily focus on him if they want to take advantage of that thread, there'd even be an easier way for Robotnik to trick Knuckles considering he could play up the whole "your tribe basically died because of Sonic" sob story.
That said, the one big plot thread the movie did leave us off with outside of just Tails was that Eggman preserved Sonic's Chaos powered quill, and if that's not an obvious teaser at Metal Sonic then I don't know what is. Sure, he uses that quill to power up his machines but it's pretty obvious he's going to have to come back with heavier artillery. The experimenting with that Quill could also be what leads him to start using animals to build his robot army, and just like Tails, in the actual video games Metal Sonic was a concept that began with the second entry; both the actual Sonic 2 we got and the game that was originally going to be Sonic 2 (Sonic CD), so it'd be apt for him to make an appearance.
So yeah, I'm thinking either it'll be Robotnik and Knuckles, or it'll be Robotnik and Metal Sonic. Leaning the latter for the time being, since the heavy lore stuff might be something they start exploring in the third entry.
