Wow, great work! I know it's a terrible place to start, but I want to start with what I don't like, LOL!
I don't like the bat. I don't know why, it doesn't mean it wont grow on me, but I have yet to come up with a better early alternative. But this is pretty dang freaking cool.
I'm for the Ranger. The ranger departs from the idea of "brans vs. brawn", but I'm ok with that. I've been considering changing the name of the tech tree altogether to something along the lines of "Four Paths" (although I don't like that particular name), diverging further from the original magitech concept. The primary reason is the religious side having para-normal powers. But the concept of starting out with a brains vs brawn and progressing into dark magic vs. natural magic and religion vs. science I think is very cool. Thus, introducing a ranger, moves the natural magic one step away from pure finger-waggling and more towards what "tech" starts out as, where as religion does the same in the opposite direction.
I LOVE the way you are manging the ancient armor! I just want to note that "Lingering Spirits" was originally (and is in the tree now) the upgrade that allowed morphing a necromancer into a Lich and required that you build a Graveyard. I enhanced it so that it also improved the now "ghost armor" only to help keep that unit from becoming obsoleted. The idea of the Lich is that they learn how to circumvent death, at some ghastly price that they won't ever admit to having had to pay (loosing their soul or something). So the idea of the the upgrading being called "Lingering Spirits" is that they learn about remaining in this world after passing. Right now, the LS upgrade isn't attached to anything. What it if is what allows morphing an ancient armor into a ghost armor and also is required for the Lich in some way?
I like requiring the study of necromancy before being able to build a necromancer tower. This elongates the process you have to go through before you can actually create necromancers. Just remember that the Path of Nature and Path of Corruption are also upgrades themselves that are quite slow, so we don't want to have to make them wait too long.
What is "Intimidation"? Would this be the same effect as "Shroud of Trepidation"? If so, I actually think that it belongs where you have it, in the necromancer tower, rather than the graveyard where it is now.
I like the Graveyard-Crypt chain of progression and I agree that the Lich should be a little harder to obtain. I'm not too crazy about your earlier idea of requiring that the crypt be charged by necromancers dying however.
I like having zombies researched at the graveyard, that makes much more sense.
You don't have corporal theft upgrade in your tech tree, this is the upgrade that allows zombies and skeletons to steal 8% of the damage done from each attack (it's automatic). This upgrade may need balancing (it may be too weak right now), but I think it's a rather nice feature. Is this the same as "Life Steal" or did you have something else in mind for that? Another upgrade I don't see is the existing "preservation" upgrade, this is a pretty big one for the survivability of skeletons, zombies and liches.
On to the items being removed by choosing one path or the other, I like the basic idea, but how do you propose we deal with those units & upgrades if they have already been created/researched prior to the choice of one over the other? Should they be taken away (i.e., the units immediately die or perhaps they slowly deteriorate) or should they be allowed to remain? Either way, this does indeed open the door for developing out along a purely "magic in the middle" path as you mentioned before (i.e., not choosing a path). Perhaps if you develop out some point without choosing a path that the option is lost to you? Lots of good ideas here!
And then on the Stone Golem vs Tower of Souls, I agree that the Tower of Souls is a more "corrupt" concept and that the Stone Golem is a more natural concept, so I can't argue with this at all from a story line standpoint. However, my main concern is with defense "structures" against air and land attacks. I like that the Stone Golem is a fairly, but not completely stationary, heavy defense unit. My original thought was to allow it to be transformed into some non-stationary, ground attacking unit on the corruption side in lieu of reason getting walls, bastions and better defense towers and nature getting their various defensive trees & treants. Yet, somehow I like the tone of your setup more, as if the stone elementals refuse to follow the player down the corrupt path they have chosen. Air and Storm Elementals may be sufficient to make up for the loss of the tower of souls, but we may still need some ground-defensive structure on the corruption side.
Also, do you think the morph from Behemoth to Dreadnought should be restricted to corruption only? Since morphing the behemoth will result in a unit with a weaker defense and the behemoth is the corruption side's "tank", perhaps we can allow them to morph into two different units, the dreadnought and some type of armored behemoth? As far as implementation, I want to keep things as balanced as possible while we progress, so with the corruption side being the most flushed out in the implementation, this will probably be one of the later things we'll need to worry about.
I have an idea for the Archamage Tower's "Energy Focus": reduce or eliminate splash damage to friendlies! This would make the archmage a truly powerful unit.