IMO If you are a typical thru hiker its hard to beat a pocket rocket type canister stove with a properly designed home made heat shield is the way to go. You can still use one without a heat shield but it increases fuel use and reduces its utility. Any sort of breeze or wind will cause a big increase in fuel usage and most folks will end up trying to find a sheltered space to cook in. Once you rig up a proper shield, breezes and wind are not an issue. One major trade off for canisters is that irresponsible hikers like to abandon empty or near empty canisters. I have even found them in fire rings.
Note many folks are willing to tolerate the limitations of alcohol stoves and are quite happy with them.
For group use or cold weather use, hard to beat a a MSR liquid fuel stove. They do require some education and maintenance, the stories of the bursting into flames are almost always operator error or lack of maintenance.