Ideally you would have a small battery for bursts of power. The fuel cells would power normal flight and provide a small charging current to the battery. When you need extra power (such as for takeoff or sudden obstacle-avoidance maneuvers) you would draw that from the battery.
You need a speed controller for each motor anyway. If you decide to use a brushless motor you simply use a brushless speed controller (it has 3 motor leads instead of just 2). So this is a wash.one thing with brush-less motors is they are usually two or three phase so you would need a few more diodes and i would use a switching regulator
To get 1 hour or more of flight time is going to require several kilograms of batteries. At that point a fuel cell becomes very attractive.I honestly would keep it more simple and use batteries and have spares ready for swapping out
Granted, some of the higher-end stuff is probably more expensive than the average hobbyist can afford (no idea what the Aeropak-1 I linked to above actually sells for, but I'm sure it's not cheap), but you can definitely cobble something together using smaller fuel cells designed to re-charge tablets and I-pads for a very attractive price. A quick Google search shows that these guys have the Brunton unit for $77.25, although it's out of stock at the moment. That Brunton unit delivers 5 volts at 2 amps, and a single fuel cartridge is good for 9 amp hours.
So for a reasonably-sized quad, 10 of these units stacked together would deliver 100 watts of continuous power for 4.5 hours while weighing in at just 2.4 kilos (total weight). That's half the performance of the Aeropak-1 for a cost of less than $800. Sounds pretty affordable to me - especially compared to the cost of some of the nicer quads these days.
The real question is this: How much power does the quad need for level flight, and how much excess lift capacity does it have?
Adam
EDIT - PS: I think the reason we haven't seen more of this sort of thing done is that the thought of piloting a quad for an hour or more is a daunting task. I get tired after just a few batteries (average time per battery is around 7 minutes). Trying to concentrate on flying for 60, 90, or 120 minutes sounds really hard. And if you're talking about flying via first-person-video, that's even more challenging.
2nd edit:
And yet no one else suggested it here in this thread. Perhaps it's not quite so obvious? I'd at least do the math on it before you dismiss the idea out of hand.