Actually, they shouldn't be able to fight Brak Eggman until Act 3, but instead, you should see him blocking your way through in some manners:
In act 1, he will fly sometimes in the city and shoot things at you.
In act 2, you will be chased by him in that highway and shoot things at you again.
In act 3, well... you fight him.
Also I agree, there should be some sort of a car gimmick, like a car that can plane through big pits that Knux and Sonic couldn't get through, or a car with a spring that can go high and reach other roads or even the top of buildings.