Another simple solution is to choose between the batteries with a simple SPDT switch, but bypass each arm with a (non-ideal) diode (regular silicon, or Schottkey). That way, (1) there is no voltage drop on the line from the battery that is chosen by the switch, (2) there is never any current flowing from one battery into the other, and (3) if you are too busy flying to notice that your chosen battery has run down, and thus fail to switch to the other battery, everything will keep running from the second battery anyway, albeit with a drop of about 0.7 volt or less (which is OK while that battery is still strong).

Disclaimer: in my glider I use a single battery, and in the rare cases where its voltage gets low, I turn off non-essential equipment (and stop yakking on the radio :-)