I agree with that the tech tree is strange. There is, as you say, only two (or three) feasible options as starting techs: Agriculture or Mysticism (the third beeing Fishing). I totally agree that more than one food tech should be available as the starting techs.
Pazyryk's list:
Ag (clear forest) --> Calendar --> Festivals (reveals wine, winery)
Animal Husbandry --> Horseback Riding
Fishing --> Sailing, Cartography (explorer,*)
Exploration (camps) --> Hunting --> Animal Handling (hawks)
Crafting --> Mining**, Masonry (roads)
Ancient Chants --> Mysticism, Education (--> Writing (open borders))
My suggested changes:
Ag should not be able to clear forests. Although that may be true historically, it has two impact that makes this a bad idea. First, ag is probably the best food tech as it is (Fishing may be better in some cases), since farms can be built anywhere and gets better later, so there is no need to make ag even better. Second, forest clearing should come later in the game, after mining is teched, so as to not circumvent the problem with forests too easily.
Cartography should include map trading! The name might be a bit misleading otherwise... (Come to think about it, native people have maps way earlier than everyone else. What is the secret?

)
About exploration and road building... Why not include a new type of road that only connects resources and towns, but do not make units move faster? Call it Path instead of road, and make it take only half the time compared to roads to build. This could be available in Exploration. Then, proper roads could (and should) be included under Masonry. Also, upgrading a Path to a Road should only take half the time required to build a Road.
I have no problems with including Apprenticeship under Crafting. It fits really well. I would like to have wine here as well, though, as in the current tech tree.
Otherwise, great work!

Much better than the current tech tree. I like that camps are available with exploration.