Originally Posted by Badger6

The benefit of upgraded wheels, on a road bike, usually means lighter weight, and often some sort of aerodynamic rim profile.

These two things added together will change how a bike rides and handles in a positive way. Often the financial advantage to upgrading only the wheelset is that (a) selling a used bike usually nets very little money in relationship to the original cost of the bike, and (b) to get to an "upgraded" wheelset on a bike, often you'd be looking at the top one or two models in a model range, where buying in the midrange and then buying a wheelset may only be 60-70% of the price of the top end model, and the quality difference in components from the mid to the top is not nearly as stark as the wheels.

Keep the originals, shod them with a different set of tires for different riding. Cobblestones, for instance, or riding the farm roads that turn muddy when it is raining here.