^ the fact Nintendo had to use Sonic The Fighters as a reference only showed what little imagination they had for his moveset..
I think this was actually a brilliant move, why wouldn't you reference Sonic's first fighter in his SSB moveset? I interpret it as being creative because plenty of characters (including ones like Mario) just have random physical moves added onto their moveset without being related to the games. Sonic, on the other hand, usees moves ENTIRELY from his series in some way, shape, or form, and mostly from the two fighters in the series, Sonic the Fighters and Sonic Battle.
While they could have done more to make his side B, down B, neutral aerial, and dash different, the latter three are perfectly accepable. Side B really should have been something else, but like you said, Sonic didn't have much going for him in a 2D plane of gameplay.
For those that don't know, his jab (punch rush until he connects with something, and then the "punch kick" move), dash (super spin dash, technically from Sonic 1, but it only goes a fixed distance like in StF), forward smash (windup punch), up tilt (skip kick), down tilt (leg throw), down smash (spiral spin), neutral aerial (air spin), back aerial (leg throw [in air]), forward aerial (emerald dive), pummel (Kick), down throw (head spin), and wall jump (wall jump) all come from Sonic the Fighters.
The few that didn't were the Homing Attack (which is from Sonic 3D Blast), Spring Jump (from the original), down aerial (which is based off his falling animation in the Sonic Advance series), Spin Dash (>B, Which is based off of how his super spin dash behaves in Sonic Battle, complete with the ability to bounce in place), Spin Charge (Sonic 2), Up Aerial (which is based on the flipping Sonic does in Sonic 3 when he's launched off a spring), forward throw (Sonic Battle), back throw (also from Sonic Battle), and down throw (which is him just ducking under his foe, with an exaggerated body shape [kind of like how Mario's fist grows when he does an F-air])
Here are Sonic's moves in that game, for proof.
His running animation was another great nod to the older games. The "figure eight" he creates by running in place was actually how his spin dash looked in Sonic CD when you charged in place (like in his taunt) or if you were running. His crouch, jump, skid, idle (foot tapping), and edge animation all come from Sonic 1 aswell. The effects used on his side B and down B moves are based off of the ones you see in Sonic Advance, you can tell by the "spikes" in the glowing effect.
The developers did their homework with Sonic.
Also, I believe that Wolf was made after Sonic, he's the only character in the game that doesn't have a beta/final victory theme directory.