While an attractive idea, I think you will find that the batteries will eventually have an uneven state of charge.  In fact, one may end up fully charged and the other fully depleted.  The problem is not on the discharge cycle, it is on the recharge cycle.

The reason this happens is that any two batteries will have a small difference in internal resistance.  When the batteries are being charged (normally right after the engine starts), one of them will suck up more energy than the other.

What I don't know is what happens when the first battery is fully charged.  Will the extra energy "spill over" to the other battery until it, too, is fully charged?  (Think of filling up an ice cube tray from one end.)

You can certainly run an experiment in your garage.  Set up two batteries in the manner that you suggest.  Run something (a big light bulb?) from one battery for twice as long as the other.  Use a hydrometer (auto parts store) to measure the state of charge.  Recharge them in series.  Measure the state of charge of both batteries.  Leave the charger on for a while and see if they get closer to each other.

An alternate approach is to ask a battery expert.  I used to work with a bunch of them 13 years ago, but not any more.

- Rob Wolf