The way I understand it, a PWM controller will use its pulsing ability to reduce the solar panel's voltage output to the voltage desired for charging the
battery; if the voltage is being stepped down from, say, 17V to 14V the potential of those 3 extra volts is wasted. MPPT controllers can convert most of that extra voltage into extra current (I'm over-simplifying somewhat) to hasten charging a little bit.
I've read that although MPPT will squeeze out this little bit extra charging current, the MPPT controller will also have a little more loss because it uses a bit more energy in order to function than a PWM controller would use. The general feeling is that for small solar systems there's no net advantage to MPPT, but with 400W-500W or larger systems the MPPT should definitely come out ahead.