Both the Boom and Classic versions of Sonic are differently proportioned. Boom's far taller and Classic is canonically shorter; I'd see Classic being most likely if they can somehow make him the same height, and possibly shorten his hair a bit (if the hitboxes aren't affected by the hair).
At best, if they reference Boom, Sonic would likely be wearing a scarf, if not the shoes and athletic tape, as well, but I think it'd look more along the lines of "Modern Sonic in Boom's clothing", rather than a "Shorter Boom Sonic".
If we're talking based on proportions alone, then Riders Sonic would be the most likely candidate, as it's literally Modern Sonic with a change of shoes and extra shades/bracers.
I could also somewhat see Darkspine being referenced, (Fur recolored darker possibly with stripes/shoes recolored blue/bracer rings but not blanking out Sonic's eyes or changing his shoe shape) but not completely Darkspine Sonic, since it's a super transformation.
A similar deal with Excalibur (it's a transformation), except, the plated armor would alter his proportions ever so slightly. It likely would also somewhat hinder him from fighting normally, as again, it's plated armor; pretty heavy to be wearing to a fist-fight for a fast, light attacker.
I wouldn't count SOAP shoes as being too farfetched.
I'd see the Link costume as being likely, as well, considering it's based off of a Nintendo character and was released recently into a Nintendo-exclusive Sonic game.
Overall, if the proportions won't be a problem and can be changed accordingly, I think that the 3 alts be be in this order of likeliness (as well as what I personally want):
1. Boom Sonic - As I mentioned earlier, I believe it should be made to look more like Modern Sonic simply with Boom Sonic's clothes. (Hair and proportions of Modern Sonic retained, without blue arms and possbly with cleaner gloves and shoes aka a bit less bandaging) Since Sonic Boom is Nintendo exclusive and releases close to when Smash overall releases, I'd see this as the most likely option, if not for the sake for more representation.
2. Classic Sonic - Actually, I believe he could be made closer to how he looked in CD or Sonic R; taller than the first representations of Sonic (and the one in Generatons), but maintaining the classic colors and sole-less shoes. Classic Sonic is a staple to the evolution of Sonic as a whole, so he'd be close to, if not just as likely to somehow be referenced as Boom Sonic.
3. Riders Sonic - Riders was a spin-off series, somewhat like Boom is, except it was nowhere near as hyped, nor did it give a significant change to Sonic's appearance. Even though this would be the easiest to implement, Free Riders turned out to be Kinect exclusive, and the previous 2 Riders games weren't even Nintendo exclusive. Basically, he'd be the least likely, IMO, because he'd be the least significant version of Sonic out of the 3. Classic Sonic is Sonic's prime and Boom Sonic is in a new alternate timeline that takes Sonic in a rather different direction.
Even though I dislike the look of Boom Sonic himself (dem legs) I'm putting my vote to a Boom-inspired alt, as I'd like to see Modern Sonic in a cool scarf :D (We could do without the mummification, though)