This has been perplexing for me. When I weigh the MSR Whisperlite with an 11 ounce bottle (full), I get approximately 21 - 23 ounces. When I weigh my Jetboil with a full cannister I get approximately 19 - 21 ounces. Beyond convincing me to order a new scale (nifty electronic scale coming to me as a result!), I can't see much in terms of weight savings between these two. I have not found an appreciable difference with these stoves outside of the Jetboil doesn't like cold weather and wind.
There are some lesser weight cannister fuel stoves at about 15 ounces with the small fuel container, but without the heat exchanging technology like Jetboil uses, fuel consumption will be likely be higher and more fuel is likely needed. Carrying a second cannister of fuel would mitigate any weight advantage if thats the case.
I have heard about problems with resupply and people using alcohol and cannisters, but not sure how much of a problem this is over a long distance walk versus white gas, kerosene, or unleaded gas. Isylvein had a good question, has resupply and availability of fuels ever been looked at along the AT or other long distance trails?