One way to replace the alternator would be to use NiMH batteries. You can get large form-factor ones at 1.2V each, and put enought together to give 13.2V or 14.4V. You could have a switch on the dash which either:
(1) Runs the alternator together with the normal car battery
(2) OR disconnectes the alternator and runs off the NiMHs.
The NiMHs could be charged at home and would give a period of time without using the alternator, especially on short journeys. The challenge would be to get the most out of the batteries by reducing electrical load e.g. higher efficiency fuel pump, LED lighting inside the car + maybe tail lights, HID headlights at night, etc