This is an interesting topic. I've never been without a car, but I would say more often than not I'm "upgraded" to a bigger car, one that I would prefer not to have (both for gas mileage and because I just like driving smaller vehicles). But I've always just taken what I get. And occassionally I'll like what I'm given (once after I booked a sub-compact they gave me an Escalade; I'm not much of a car guy, but that was kinda cool).
I'm not sure if there's a great answer for this. Booking a 2nd reservation seems like a bit of a hassle, altho maybe it'd be worth it in some circumstances. But if everyone did this, imagine how much worse the situation would be.
The only other "solution" I can think of is to call the rental company before you get on a shuttle to see if they have cars. That would save you a couple of shuttle rides (admittedly, not much). tls