Overall brightness is primarily limited by the regulation circuitry in the light. Some circuits can handle more voltage than others and may permit a higher change in brightness when an additional cell is added (i.e., Surefire 6P with an A19 cell extender) or, as mentioned above, a rechargeable cell with slightly more voltage output is used (i.e., 3VDC from a primary vs 3.4VDC from a rechargeable). Again this is limited by what the circuitry can handle.
Some lithium battery manufacturers have more stable outputs than others which can provide longer run-times at a given brightness, ensuring better efficiency in output, but not necessarily brighter output. For example, manufacturer A may last five more minutes at max output than manufacturer B, but both will only ever give you a maximum of 6 volts in a 2-cell configuration.