This sounds like a good opportunity for a startup. You wouldn't even need to establish a counter at the airport. As a customer, you just check-in via Blackberry, iPhone, or even text message. The shuttle bus swings by to pick you up and you're off.
I was thinking the same thing. What a fantastic opportunity for somebody to build a centralized, remote system, that's easy to use and offers some really powerful features ("Hi Mr. Jones, would you like the same kind of luxury sedan you rented last time? A local map and directions to some common destinations is already on the front seat for you."), and then sell it to the rental car companies.
Heck, if you can collect the arrival times from the various airlines, you could send a confirmation message a few minutes after the plane lands. Checking in would be as simple as hitting reply.
That would require the traveler's flight information, which I wasn't assuming was something the rental software would have access to. However, if the customer wanted to offer it up ... sure!
Higher-end hotels have systems that do this kind of thing already, and there's no reason that rental car companies couldn't also.
