The weakness of the Incredibles is they have no one to match Reeds intellect.
However the Incredible's powers, particularly Violet's and Jack-Jack's, are the real threat.
I think Sue, sees Jack-Jack as a cute baby, and picks him up, and turns invisible to keep him out of harm's way. Jack-Jack morphs into his demon form, and lights out for Sue.
Johnny probably couldn't hit Dash with fireballs, but he could put up a flame cage and trap him. However I think Dash could get out by vibrating so fast that he extinguishes the flames of the cage. Then he could run around Johnny, doing the reverse vortex thing, and suck all the air away from him. Johnny without oxygen, is an unconscious super hero.
The Thing could probably hold his own vs Mr Incredible, but once Elasta-Girl or Violet jumps in, it's either nap time with a force field around his head, or Elasta-Girl wraps him up enough for Mr Incredible to deliver the knock out punch. However, if Reed was able to wrap up Mr Incredible, and Thing was able to somehow overpower him, they might have a chance, but it's still a numbers game, and the Incredibles would be ahead at this point. But Reed and Ben are a pretty formidable team.
Jack-Jack could probably burn Mr Fantastic, if Reed was silly enough to pick him up after seeing what happened to Sue. Since Reed's a genius, I doubt he'd do that. Dash would be too fast to catch, but probably couldn't hurt Reed. Elasta-Girl and Mr Fantastic would be a draw. Mr Incredible, if he's still conscious, probably couldn't hurt Reed either.
But I do think Violet could encase Reed in a bubble, and compress it down till he's not able to breathe. And while Reed is terribly smart, I don't think his power set is able to directly hurt anyone on the Incredibles' team. He might be able to slow down Mr Incredible, but everyone else on the team he really wouldn't be effective against. Unless he has some sort of device that allows him to nullify The Incredibles' powers, Reed just can't physically do much against the other team.
Finally, if Ben wasn't taken out by the team of Mr Incredible, and Elasti-Girl, I think her and Jack-Jack put him away. Elasti-Girl plays "Catch the baby" with Ben. When he catches Jack-Jack, the baby turns into his metal form, throwing the Thing off balance. Elasti-Girl, then wraps herself around Ben's head, and it's lights out for the Blue-eyed Thing.
I'm going with the Incredibles. If Sue had her force fields, it might be a more even match up. But even then Jack-Jack's powers are largely undocumented, and would probably provide the edge.