The benefits more than make up for those costs, ensuring those who benefit also contribute to upkeep is a delicate balance but things like congestion pricing can go a long way.
Part of the solution is to have more freeways and thus spread exits more evenly across the city. Another part is to adjust city streets around those exits so they can accommodate a large influx of traffic. Similarly you optimize traffic flow inside the city by eliminating things that limit flow like street parking etc.
Going at least a little 3D is definitely required, but not necessarily big dig levels of 3D.