I take issue with the notion that two, three, or four batteries in parallel will not charge ALL batteries to their full capacity. Why? Because the charger cannot tell which battery is full and which is not. It is monitoring the system, not an individual battery. Parallel systems have been used in diesel powered cars and trucks for decades and if that were an issue an alternate charging system would have appeared long ago. Here are a couple of references the nay-sayers may want to read.
From Superior Battery Manufacturing:
Batteries may be connected to the charging source in series, parallel or individually, depending upon the type of charger used. More than one battery (all must be of the same voltage) can be charged on high-rate fast chargers. When this is done, connect the batteries in parallel, i.e., connect the positive (+) terminal of one battery to the positive terminal of the next battery and negative (-) terminal of one battery to the negative terminal of the next battery, etc. The number of batteries that may be connected in parallel depends on the current capacity of the charger. The output of the charger will divide equally among the number of batteries in parallel if they are identical (same rating, same state-ofcharge, etc.) and there are no high resistance connections. For example, if five batteries are being charged in parallel, and the charger output is 20 amperes, each battery will receive 1/5 of the total output, or 4 amperes.
And you just might be interested in this device which does exactly what is not being recommended. This device just happens to be made by one of the major battery charger manufacturers in the country.
http://www.centurytool.net/6075_300a_Bus_Bar_Kit_10_Pair_p/aso6075.htm
Lastly -- just what do you think a combiner and a switch accomplish? They both allow charging two batteries, or two parallel banks from a common alternator. This is simply not an issue unless you actually have one really rotten battery in the system and that should be obvious without even using a charger.