If your residential and industrial zones are separated, as they should be, you need to make sure there are multiple roads between them. All the transportation funding in the world isn't going to help if all the cars going between Industrial and Residential are bottlenecking on the 1 or 2 (or even with more, depending on the size of the city) roads between them. Make sure there are enough roads connecting the places in your city, make sure it never depends on just 1 road at any point, because that is what causes traffic. As for zones, you don't want them to be huge, but as long as any individual tile in a zone is more than 3 out from a road (meaning no more than 6 between roads) you should be fine.