I've used both setups, but never performed any objective tests on fuel usage. (I've since given away my Snow Peak stove and pot, so can't do so now.)

As far as weight, you will save a few ounces with the Snow Peak setup - though not as much as you'd think, since that windscreen appears to be steel (why not aluminum or titanium, I don't know.) Snow Peak's website says it weighs 2 ounces, but I remember mine weighing more like 4.

Based on pure conjecture, I believe the Jetboil is the more efficient stove. Even with the windscreen on the Snow Peak, there seemed to be a lot of heat escaping up the side of the pot; my handles always tended to get warm, and I could "see" the heat waves. I don't notice either of those things with the Jetboil, which makes me think it is more efficient at putting all the heat into the pot. Also, the Jetboil neoprene cozy appears to keep the heat from dissipating as quickly.

I'm sure there are others who can do a better job with the science than I did. However, my main reason for choosing Jetboil over the Snow Peak was that the Jetboil system simply fit my cooking style a little better, and my food stays hotter longer after the stove is turned off. The weight savings kind of faded into second place in this case.