Lots of good information in this post. The way I see it, is what are your primary uses for it going to be. If you want a quick light setup to boil water then the Jetboil is a good choice. I personally try to stay away from any stove that I have to physically build a fire, will they get the job done, sure they will. But, how much time do you want to spend messing around with a fire, especially when you are up early and to bed late.
However, what if you are going to want to use the stove to do other things that just boil water? Things like large pots and frying pans, then you may be better off buying just a stove and outfitting it with various cookware assortments.
Last, what type of fuel source are you going to use, liquid fuel (white gas..etc.) or do you want to stick to canisters. The nice thing about liguid fuel is that it tends to perform better at higher altitudes and lower temps, and you can refill at your convience. Canisters at least to the best of my knowledge cannot be refilled.
For the reasons listed above I have a Soto head that I will use with canisters if I am looking for light weight and boiling water. However, if I am looking to get more out of my stove I use a MSR Whisperlite Universal. The nice thing about the MSR is that I can run it off canister fuel or liquid fuel, all I have to do is change the jets in the fuel system. Also, the base and holding tray on the MSR are built to hold bigger pots and pans. The downside is that it is a heavier setup.
I really do not like the ignition switches on the Soto or the Jetboil I prefer to have a stove that you light with a match. I am sure you will get different opinions on this, but I have seen the ignition switch go out on the Jetboil on more than one occasion. Sure, it can be replaced, but only if you have a spare with you.