You might get more useful feedback if you expand a bit on what you mean by "doing some thru-hiking". By "some", do you mean you plan some section hiking, or maybe you plan to start a long trail and see how it comes out, maybe do it all, maybe not, or ... ? And somewhat more importantly to gear selection, which long trail are you considering? I think that hammocks are a lot more common on the AT and the long trail in Florida than on the PCT or CDT.

I thru-hiked the PCT this past year and considered swapping to my hammock for the more northern stretch, but a combination of experience (shake-down trips) and analysis made me conclude that I was better off with a solo tarptent.

A hammock is certainly do-able in a lot of stretches, and I did see one guy start out (at least) with a hammock, FWIW. Bottom line is that I agree that it's hard to be weight neutral and stay reliably warm enough, plus there can be places where despite a lot of trees it's hard to find a decent place to hang. I recall one long shakedown hike along the PCT in WA state when I found more frequent tent sites than I did hang sites, despite lots of trees ... either too much brush everywhere between trees, or new forest with trees growing close together and lots of thick understory branches down to the ground.

I think the key thing to decide on hammock vs. sleeping on the ground is *why* you're inclined to a hammock. If you just can't sleep any other way, then of course do what you have to to make it work.

Stove: search various forums on stuff like this and you'll doubtless find existing long threads; alcohol stoves are more popular for thru-hikers, at least on the PCT, due to availability of fuel, plus perhaps not having to mess with partially full cannisters.

Pack: I too used a GG Mariposa Plus, and it worked great; stretching (stressing it) a bit to use with bear can in the Sierras, but it worked. ULA makes some great and popular packs too.
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Brian Lewis
http://postholer.com/brianle