You're quite right that connecting 2 batteries in parallel halves the internal resistance. However, it's not significantly different than connecting a single battery of double the capacity.
Two 6 volt in series to make 12 volt ( or two 12 volt to make 24 v ) have inherant problems. No two batteries are identical, so the volt drop across each when charged in series are differant, so the charge to each battery is differant, and the recharge level is differant. You thus end up with one battery charged to a lower level, resulting in reduced battery life. Secondly you should always change as a pair, changing one battery in series will result in a bigger missmatch, and killing one battery.
To Sailfree. Two batteries in paralell is no different to one battery twice the size. If a large battery is very flat then it takes a large current from the standard alternator regulator set up.( designed to run the alternator flat out untill battery voltage rises to 14V.) This could potentially damage the alternator however in practice the resistance in the alternator will limit the current to something like its rated output current. of course the battery voltage usually rises quickly to reduce the current so that you are back to the usuall problem of not getting enough current into the battery to quickly charge it. Of course larger battery will accept more current at a given voltage just the same as 2 batteries in paralell will take twice the current of one. So an alternator rated at 55 amps will be struggling to give 55 amps and probably only then at a voltage at best around 12 volts. It is not a safe rating but a capability rating. regards will