I don't think any tree should block two other trees.
I also think that elven craftsmanship is a fantasy staple; elves might live in Nature and all that but still make fine things and produce high quality weapons and armor.
Sounds reasonable, you convinced me

So in my current plans there are 3 pairs of exclusive trees and 4 non-exclusive ones.
I think the expansion mechanics have a lot of promise for a fantasy mod; a fantasy world offers so much more scope for religion. I could imagine for example that you could choose different spheres of influence for your god, like how Dungeons and Dragons clerics (I'm thinking 3rd Edition, never played anything later) could pick a couple of spheres from a long list of things like Good/Evil, Healing, Fire/Air/Earth/Water, Travel, Order/Chaos, Dreams, Magic, Sun, Nature, Weather, Protection, Death, Tyranny, etc.).
Different aspects could have different game effects.
And then you could have different aspects of the Church: evangelism, monasticism, militant, and so forth.
So a really religious civ that produced lots of faith points might get a religious faith that has lots of powerful abilities.
The mechanics seem promising.
Yes, the customizable religions sound promising, also I thought about using Faith as Mana that can be used for different magical things, not only religious (and renaming the Mana strategic resource to Magical Power). But I don't know how feasible it will be, we'll see when the expansion is released.
But how does that change your play-style? Every game plan will use agriculture and population growth, no?
Maybe this should be about rapid expansion? Free worker/settler/build speed effects, rather like Liberty?
Or bonuses in cities you found (as opposed to those you capture)?
There are other sources of food than farms, I'm going to enable building Camps in all Forest and Jungle tiles to get more food from them, as an alternative to Lumbermills that give you production (and disable Trading Posts in forests and jungles). So Camps will be the main source of food if you go for Nature instead of Development (I'm also thinking about renaming it to "Civilization", maybe this is the name that Pazyryk can use in his mod too?) Camps will give less food than Farms, but bonuses for Forests and Jungles from Nature will make them worth building.
There will be a policy that gives a free Worker (or two) in Development, and another one that increases the work speed of Workers (I planned to put it in Craftsmanship, but now I think I'll move it to Development, as linking these 2 policies together seems logical, and increased worker speed doesn't fit your "Elven Craftsmanship" vision

). Settlers are a "different pair of shoes" in my mod, as you'll always get them for free when you have enough happiness to support a new city (as I already wrote in this thread, this is mainly to help the AI, which often "forgets" to build them).
As for bonuses for cities that you found, I have no such plans for now, but if you have a good idea how to implement them, I'll consider it
Other bonuses are going to have to be really powerful to compete with "larger population", because larger population gets you more of everything.
Including more unhappiness

And sometimes you won't have enough productive tiles or specialist slots to use for all that population... (Btw I'm thinking about reducing the maximum city radius from 3 to 2 so cities won't grow too big, is it possible without the DLL code?)
Not really very coherent IMO; more gold is always useful for any strategy. Gold in Civ5 lets you do almost anything. What should you focus *more* on with a Wealth strategy?
Some possibilities might be: gold boosts from a particular improvement type (so you build that improvement type more), boosts from luxury resources or the buildings they enable (to encourage you to settle near those), interest income on stored gold (to reward you for hoarding gold).
Gold boosts from improvements (Trading Posts or something like that) and happiness from buildings that require some resources (like Mints) are planned, interest not.
But more technology is good for everyone, and winning combats is good for everyone.
I think it works better if it boosts technology from playing in a particular way; if boosts technology buildings (so changes which buildings you construct), it makes magical research cheaper (so changes which techs you reseasrch), it makes it cheaper to build/use mage units or makes these units more effective (so changes your army composition).
Yes, I never planned it to give only simple science boosts, as always different policies in the tree should have different and interesting effects.
But more happiness is good for everyone. What kind of playstyle does it encourage?
You can encourage an annexation or a puppet playstyle by rewarding those kinds of things (eg by boosting yields of courthouse building, or by boosting yields of a puppet building - I strongly recommend adopting Thal's VEM mechanic whereby puppeted cities get an automatic building that reduces their yields, and is removed automatically when a courthouse is built; going puppet-crazy is too advantageous in vanilla, there needs to be more incentive to annex).
I'm going to remove puppets completely, I don't like them (I already did it in my non-fantasy experiments with Civ5 by using some LUA code that changes all puppets to annexed cities every turn). As for the playstyle that it encourages, I'm not sure, but I think it should be a different style than Freedom, which is focused on culture and specialists, so it will be probably more "wide" than "tall" style, as you can have more cities, and many of the happiness boosts (for example happiness for garrisoned units) will depend on number of cities.
Not normally a very powerful benefit, particularly for the human player.
The others seem fine.
Chaos could also boost demons, if you're going to have those?
Order and Chaos are the least developed ones for now, they still need work to make them give interesting effects. As for demons, some civs will have access to them but not all, so a policy that boosts them would be useless for some civs... But it's an interesting idea to consider, if I can make it in a way that is beneficial for all civs.
I also notice no city state boosts anywhere. Not part of the plan?
Like military benefits, they will be distributed among different policy trees - more effective gifts in Wealth, science from them in Wisdom, Great People in Freedom...
(But, as I wrote earlier in this thread, instead of CS there will be minor civs that have multiple cities, and in the standard settings there will be less of them on map than in base Civ5, but due to more cities, territory, resources and armies they will be more valuable allies. This will probably require making gold gifts generally less effective.)