I recently went through an extended period of troubleshooting a charging problem on a 2001 LL Bean (3 wire system). To make a very long story short it was a bad alternator. It started out intermittently with several warning lights flashing, eventually total loss of charging. When measuring voltage at the battery it should read approx 14 to 14.5 volts when initially started, and depending on load and state of charge will then modulate between approx. 12v to 14.5v. When we had the total failure the voltage while running was erratic, but less than 10v.
There are people who have de pinned pin C (black/red wire), and the car electrical system works fine. Some say this is hard on the system, but apparently the internal voltage regulator in the alternator works just like the 2 pin systems in the 4 cyl cars where there is no signal at pin C which should produce approx. 14.5v with no problem. There is also some info floating around about a Subaru service bulletin for certain Foresters that changes the signal to the ECU, simulating a load, presumably to influence the signal at pin C. I have also read several reports of people trying to determine what the signal is supposed to be at Pin C, there does not seem to be a consensus on what the signal is supposed to be.
There are tons of people that have had trouble fixing charging issues with the H6 I think a lot of it is due to not understanding the system. Also the aftermarket alternators have a bad reputation. Also I don't think the local parts store can do a good test on a 3 wire system, most don't know what it is.