I've always liked 12 volt systems. 6 volt systems require larger gauge wire and higher current switches (for equivalent wattage). 6 volt systems have higher I2R losses and will have more contact resistance on connectors. 12 volt lead-acid batteries have always been less expensive per amp-hour than 6 volt lead acid batteries. With NiMH batteries, it's more practical to use a single 12 volt pack than carry two six volt packs of half the capacity. 12 volt Xenon strobes are common, 6 volt Xenon strobes are not. The only time a 6 volt system would be preferable is if you have a headlamp that uses an H3 style bulb because the lowest wattage 6V bulb is 25 watts, while the lowest wattage 12 volt bulb is 35 watts. Volkswagen switched from 6 volts to 12 volts on the 1967 Beetle for a very good reason! Read 42 Volt Electrical Systems for a discussion on wire and contact resistance. If you build a 6 volt NiMH system you should consider using C or D cell batteries for longer battery life on a single battery pack.
Remember, wire and switches are rated mainly by current. For example, 30 Watts/12 volts = 2.5 amps, while. 30 Watts/6 volts = 5 amps. You will need heavier gauge wire and may need switches with a higher current rating if you go with a 6 volt system.