Indeed, with a desktop machine one can add a card - $40 isn't cheap, but it's not a fortune. It's a little more than a Pi, coincidentally. But I don't doubt one could buy cheaper.
Unfortunately, with a laptop, which is increasingly common, the USB adapters are not much use - they are specifically for printers and can't be used for JTAG, for example.
Therefore, the Pi's provision of GPIO is a good thing. I note also that a project decision to keep the price down is specifically to make it less of an issue if the Pi is damaged in experiments. It's not primarily to make it attractive in the developing world, although it has that side-effect.
(You are repeating yourself again in giving us a paragraph on the Pi's limitations - don't be surprised if it annoys. I do apologise for any unfair criticism.)
Cheers
Ed
6502.org
The 6502 Microprocessor Resource