My latest thoughts are to build a semi-passive system using two transceivers, each relatively cheap ($12) along with an Arduino Fio and the main brain.
The Fio would be integrated into a custom-built fob with one of the transceivers, other small misc. hardware and two rechargeable CR2032 batteries along with some magic induction hardware. All this sealed up nicely in a waterproof fob, to be recharged via induction with no wires.
The fob would be in receive-only mode, sleeping for 5 seconds or so before listening again to save on battery power. I'm sure more measures can be taken to conserve battery, however these are just my rough thoughts. If a valid signal is received from the car unit, the fob will begin authentication, if not, it goes back to sleep for another 5 seconds.
I know I'm just creating more work for myself here, but this really seems like the only viable option.
I did have another idea, in which the driver wears a wristband containing an RFID tag, and the receiver would be placed directly adjacent the button, so authentication would only happen when you were ready to start the car. The only problem with this is that I'm not sure the range of the receiver would reach far enough even for this, as it would need to read about 6".
There is still much research to be done...