[mseebach]

I suspect that the reason for this is the behaviour of most OS's around USB audio devices: switch over the default inputs and outputs to the new device -- which would mean that when you plug in your modem, suddenly your Skype would configure itself to "use" that device for it's audio IO.

Also, I'm not sure how easy it would be to even configure the OS to route modem output to default sound card input (your headphones), and the same soundcard's output (your microphone) to the modem input. The assumption of most OS's seems to be that you have one active input and one active output at any given time. It's certainly not something I'd immediately know how to wire up using the default mixer in Windows.

[IshKebab]

You wouldn't have to wire it up using the default mixer yourself. Whatever program you were using to make calls could do that for you.

The only vaguely valid technical reason I can think to do it how they have is to reduce latency. Of course the real reason is laziness.