Just having taken the poll, and not having read the conversation, I think there are options missing.
I like Learn by Looting and all the magazines. I think the magazines found a nice way to draw out the game.
I like Learn by Perks. I thought that system worked reasonably well, though sometimes I am frustrated at which perks were with which abilities (like Strength) or that they're tied to an ability.
I'm okay with the idea of Learn by Doing, but not to the exclusion of the others. I've played on a server that swapped in Learn by Doing and I didn't think it played very well. Then there are the notable goofy things like crafting 100 stone axes.
Since TFP likes to experiment, I wonder if a mix of the three might be the best. I think the approaches could be integrated a little. That is, when you take some of the remaining Perks I think it could come with a little bit of magazine-like improvement, maybe as if you had read 2-3 magazines. I think there could also be some milestones that represent Learning by Doing that also generate some magazine-like points. For instance, when you craft your first iron tool, your first steel tool, kill your 100th zombie with a club, etc.
If you make me pick one, I'm sticking with Learn by Looting for now just because I want to see how it plays out over a long game. I'd put Learn by Perks 2nd. Then I'd put Learn by Doing last.