Cells typically found in "premium" power tool batteries are typically rated for 20-25 amps of continuous discharge, not 15. Conservatively speaking, the M18 9.0 can provide 18v nominal * 60 amps = 1080 watts continuously (obviously until voltage starts to dip after some use). The Flexvolt batteries can put out the same wattage (54v nominal * 20 amps = 1080w), they just use 2 Ah cells vs. the 3 Ah cells in the Milwaukee, like you mentioned. Regardless, the Flexvolt could and should easily win the run time war since it has 2 packs aka 216 watt/hours of juice. The M18 9.0 only (ha, only) has 162 watt/hours of juice. That's 33% MORE energy at its disposal, and its blade is only 20% bigger.
I think the blade plays a factor, but I don't think it's as big as everyone thinks, although I could be wrong. I guess I have a hard time believing that the bigger blade consumes that much more energy. I think at the very least, it should have the same amount of run time. But it doesn't.
This shows that the Milwaukee is more efficient. It uses the juice when it needs to, like when a cut starts to load up the motor. I think the Dewalt uses extra power when it doesn't necessarily need to, which is probably why it "feels" more powerful to most users. It's like a 400hp V8 and a 400hp turbo 4cyl - which one consumes more fuel idling and cruising? The V8. Both make power, just one is more efficient overall, only asking for the juice when it's needed (i.e. when the turbo kicks in, otherwise it's a rinky dink 4cyl out of boost).
That's my theory at least. The Flexvolt tools have potential to be more efficient since they don't require nearly as much current (amps) to make the same power (watts), and current makes heat, and heat is bad. I don't know. The Milwaukee engineers really, really did their homework because an HD 18v battery powered tool shouldn't be better than a 54v one, but it is. The packs/motors/electronics are hard to match.