I think something must be largely reworked in the city model : the too close relationship between commerce (science/tax/luxury) and nearby roads. To me, commerce shouldn't be dependant on roaded tiles, but ultimatively on the population of your city with many elements that can improve it.
I think any citizen should produce 1 or 2 commerce, and many improvements should raise the output (such as libraries and marketplaces). But also, some elements external to the city should raise the output too : if the citiy is connected to the trade network, it should receive some commerce too, and should recieve more commerce if it has several "commercial" connections : for example, the city could 25% extra commerce from being connected to roads + 25% extra commerce for having a harbour + 25% extra commerce for being connected to another city with a river etc. Also, I think CTP-like commerce routes should give more commerce to the cities they get through. Eventually, bonus tiles should give commerce as they do now, like gold or luxuries.
Such an idea will reduce the usefulness of roads and railroads, and will hopefully let the map look better.
The Diplomat :
However, I think it is good to allow normal tiles to be improved with mines or irrigation.