"Supplying voltage via the 5V or 3.3V pins [...]" to what?

Constantin:
The jumper pins are the most foolproof method, though not as convenient, and convenience / ease of use is an understandable reason for the Arduino hardware team to choose the path they did.

I'm not sure...I don't think many people will be constantly switching between power sources.

Even if they are, they still have to physically plug/unplug the external power supply (or throw a switch, or whatever).