The idea behind the capacitor is to replace a battery in a bike that has had much of the electrical load eliminated such as electric starters, lighting, radios, air-con etc.
All those things draw down on the battery when the bike is idling and not producing enough voltage to both charge the battery and keep the bike and all these extra bits going. Such as at a traffic light or in stop/go traffic commuting home from work. This is why you need a battery - to store the energy for these times of low generation.
A PMA setup generates more oomph than a stock XS650 rotor / stator at low RPM, enough to start the bike when turning it over with the kicker. The SR500 for example is a kick-only bike, and has a PMA. It also however has a battery. You can swap the battery out for a capacitor and not really change anything else and run around town (friend has a battery eliminator - expensive word for capacitor - on his SR500).
An alternative setup, if eliminating/reducing the battery size is your goal are these new lightweight lithium batteries like the Ballistic units. Way smaller and lighter than a stock battery but with all the power.
So, if your charging system is kaput and instead of spending money on rotors every once in a while you feel like spending $300 on a PMA setup, go for it. If along with the PMA you want to eliminate the electric starter, you can go to a smaller / no battery.
You don't need the PMA to go to a smaller battery however. I eliminated my starter motor and run a small AGM battery under my seat. Will probably go to a much lighter smaller lithium model at some point, but my charging system works (replaced my defunct rotor with another free used one a while ago). When this rotor goes, I'll have to choose between another used $20 rotor, a new aftermarket $100 rotor or a $300 PMA setup.