Yeah, I wouldn't be surprised if eventually the SSB Mario was discontinued & they made the "Super Mario" line version the universal one for said character. But like, if we got a new Animal Crossing, you know they'll probably make a new version of the Villager and say it's part of the Animal Crossing line instead of the SSB one despite both working on each other.The Mario characters from both sets aren't game specific, its just that they can only store data for 1 game at a time. Wouldn't be surprised to see Smash Mario, Luigi, Peach, Yoshi, and Bowser get phased out shortly after the new line's release to avoid confusion.
Or maybe, more likely, SSB was just a special case due to how many characters/franchises were in it & afterwards, they'll just do a line based on franchises (Mario, Zelda, Kirby, etc.) instead of a specific game and those will be considered the "universal" amiibo for that character. No "Mario Kart" Mario or "Mario Tennis" Luigi or whatever when it'd be simpler & cheaper to just have one version and say it's from this main series/franchise.