Yesterday I received a call from a system integrator – who has been installing solar systems using PWM charge controllers and is looking at switching to MPPT charger.  He has an experimental set up with a 200 AH batteries, 48V, 2500 Wp Solar panels : 250 Wp X 10 nos , a PWM charger and a MPPT charger which he had acquired from his recent visit to Bangalore. (Its not from AMBRT though)
He was aghast that contrary to his expectations the back up power from PWM charger was longer than that of the MPPT charger.
Questioning him further – revealed two common issues with comparison. 1) Unlike the PWM charger , the MPPT charger is expected to have a different input Voltage and current compared to its output. If the MPPT charger is working to its full potential- then the Voltage in the input is likely to be the Maximum power point Voltage – Vmpp.  If you would like to compare two chargers – they are ideally done in parallel  connecting to the same battery voltage and are extracting power from two arrays under same conditions of solar incidence.  If this is not possible, then calculate the total energy delivered – on a few days – hopefully with similar solar incidence.
Note : The wiring of the array using PWM charger may not work for the MPPT charger. In the above example, with just two panels in series, the Voltage of the array could be in the lower end of the input Voltage range of the MPPT charger , BUT the current  might be higher than the input current limit. Therefore the array may have to be rewired with 3 Panels in series instead of two in series.
2) Battery Voltage matters. As I found out in this case, the MPPT charger was not pushing the battery voltage to beyond 54V – based on settings in the charger. The PWM charger on the other hand was pushing the battery voltage to much higher – so definitely not an apples to apples comparison. What was probably happening was that the MPPT charger was backing out when the battery voltage reached 54V. The MPPT charger was then regulating to keep the battery voltage nearly constant , allowing the battery to draw as much current it wanted. The MPPT charger was no more operating in the MPPT point.
so what is the best way to compare both the chargers?
If the array cannot be made parallel and each half connected to a different charger – the next best thing is to
a) Connect the charger to the batteries on two different days – note the sunlight conditions and judge if they are similar.
b) Log the Battery Voltage and measure the Current at the output of each of the chargers in regular intervals. – Say every ten minutes – through the day.
c) Make sure a load is connected to the battery so that the battery is not fully charged. For example in the 48V system , adjust the loads so that the Voltage of the batteries are maintained at around 51V.
d) Multiply V and I and sum the values to determine the amount of units ( kWHr) of energy delivered in the same time frame. This should give you an approximate estimate of the performance of the two chargers.
Note : For the MPPT charger – the wiring of the panels may have to be changed due to the different input current ratings.