There seems to be too many cross tree pre-requisites in the tech tree to really specialise into one of the three particular paths.  I get from a "if this is a real world" perspective why Arcane Armour would also need Heavy Armour to be researched first, however from a game perspective, it caused me to not be able to specialise all the way up the magic tree (in this particular game I had tons of crystal).

The above is just one example, and the magic tree actually has the least noticed (I might not have noticed if I already had the prereq) cross tree prerequisites. The Civic and Warfare trees at the moment basically need to be researched together.  It appears to be that you can only be one level ahead on either treee before the next level tells you you need a cross tree tech to be researched before you can have this one.  Another example, Weapons (of war?), the second weapon tech on the warfare tree requires blacksmithing on the civic tree.  Both are at roughly the same place on their relative tech tree level wise.

I think cross tree pre-reqs are cool, however, having the core techs of the different trees rely on core techs of other trees stops specialisation.  Cross tree pre-reqs should enable the non-core cooler stuff on a tree, which don't have to be researched, but would be cool if you had them (a good example would be horseriding/warg riding, they aren't core warfare tech, but they allow greater differentiation of your army if you had them).

This paragraph is conjecture as I didn't look through the xml to see all the pre-reqs.  IF the first half of the tech trees are designed to be highly cross linked/pre-reqed for balance, flow, or whatever, then the UI should be changed to reflect that.  Basically All I'd suggest is have a research field called "Basic" or something like that, where you had the first half of the techs.  This would allow you to show ALL of the prereqs by the lines traced from one tech to the next.