Most mobile fuel cell systems (think cars, trucks) these days are technically hybrids. They usually use a small battery (up to a couple of kwh), the way a Prius does, to deal with rapid changes in power demand and to store energy from regeneration. Supercaps can do the same job, but can't store as much energy; they do, however, react more quickly than the battery. In an extreme situation, I would see a supercap driving the motor, backed by a battery, backed by a fuel cell taking the place of a similarly slow-responding diesel engine. Usually, though, you would only need the supercap OR the battery. And another point: the capacitor likely will last longer than a battery.