After I toyed a while with them there seems to lack something, such as subterranean rails, bridges, elevated rails and so on. And of course, a less awkward way to place straight rails and curved rails.
New ways of transportation might be really awesome: subways, ferries, planes, automated trucks, roads and the list goes and goes.
If you've played, say, Simcity 4, you've realized that most of the fun in there is managing traffic and commuting systems; why not implement this to Factorio as well? New ways to travel and move goods, more logistics strategies involving transporting of goods and players. This will add a ton of fun to the already fun game there is.