I didn't think I woul say anything, but I really want to throw this idea out there:
I think this team, if it did happen, would want to ignore one of the common principles of 2v2: Disregard the risk of hurting each other.
Hear me out. When I look at the character's mechanics, I see a striker and a defender (RPG terms). Sonic can theoretically be completely avoidant, except for stalling rules. In general, his speed (and other factors) make him as you say good at punishing, which is a pretty good equivalent for the striker role - hitting lone targets in ways that make them cringe and bring the end of the fight nearer.
Ganondorf has abilities that make it difficult to ignore him - being, his fricking powerful attacks. If he's in melee, and times his ****, then the devastation can be unleashed.
The way these two roles ought to be used together is having the defender (tank) stay on top of the foe, merely threatening to act if their attention deviates from you, while the striker weaves through range, hitting targets of opportunity, and also goes into pursuit. As well, a classic combination is for the two roles to 'flank' a target, allowing for combat advantage to both, but the inability of the target to effectively fight other than the tank. In this game, flanking would of course be actual flanking.
EDIT: Using Sonic to disrupt people "cluster****ing" Ganon would fall into this 'flanking' idea.
But smash bros. mechanics would mean Sonic could get hit by Ganon - not least because one of Ganon's hits could send the foe into Sonic for collision damage. I say that the two characters are heavy enough to deal with this, because I think this strategy will work.
If the two characters see "damaging the opponent" as the main goal, Ganon sees the minmalization of times the opponent hits Sonic as good, and Sonic considered his role to be to hit as many opportunities as possible, they will approach a winning position. Sonic should allow himself to go for K.O.s if he sees them but even if he would need to go through Ganon. The two, meanwhile, should train so that Ganon can expect Sonic to avoid being where Ganon throws his limbs, when he has to.
An important thing is that Ganon is the tank because he can physically impede attacks. He can actually get in the way of projectiles, whereas Sonic cannot. Sonic should physically use Ganon as a shield if he wants to.
Questions? Comments? Des insultes?