Flexibility.
1. Get rid of the grid and allow completely free-form road/rail/etc laying. Obviously there could still be a 'snap to grid option'. This would allow any angle and all sorts of new options (wide curves?).
2. Layers, allow a number of layers. Perhaps ground, five different layers below ground and five above. This would greatly improve the flexibility of your transport network. For instance, you could have underground rail lines (not subway) with stations. Underground highway intersections would also be possible. Multiple subway lines could pass over/under each other without intersecting (or perhaps have stations on multiple layers allowing transfers).