The risers fitted with the molex 4 pin connector take +12V and +5V from the molex. The risers fitted with the 6 pin power connector only get +12V from the connector so need an on board regulator to produce the +5V needed by the GPU. The 6 pin type is best suited for when you have a separate power supply for the GPU's as there is then no possibility of connecting 2 different power supplies to the GPU at once. The 6 pin types have more components on them to give the +5V supply and therefore have more scope for failure.
Nonsense. PCI-E GPU's only use 12V, which is what the PCI-E specification calls for. Up to 75 W though the PCI-E slot, 75 W through the 6-pin and 150 W through the 8-pin VGA power inputs. The voltage regulator on the 6-pin risers stabilizes the the 12V line to prevent spikes. It is NOT a transformer to convert 12V to 5V.
If you look at the pin connections of a PCI-e slot you will see that it also needs a +3.3V supply (I was wrong saying 5V it is 3.3V). All the 6 pin risers I have seen have more components fitted than the molex types. I can only think that it is easier to derive the 3.3V from a 5V line than it is from a 12V line.