[EDIT: Looks like I agree with what other folks have said [e digicons]:thumbsup:[/e] ]
Here are some suggestions along the lines of this discussion considering most folks are ok with the current standing of the Civilization tree (I've never seen any arguments against this assumption.) This rambles a bit, sorry for that.
The Warfare tree could have a Hunting line of techs. This line could introduce certain weapons and armors (bows, daggers, hunting knives, axe, and spears ought to be unlocked earlier; also hides and leather armors), buildings (for instance a Hunting Lodge building tree which can only be built on forest but gives food per grain), and unlock some unit traits. Then there could be the more traditional Warfare line, Which would be all about unit training, smithing, production (especially unit production, but not completely), Weapons of War (swords, battle axes, warhammers, advanced polearms, etc) and advanced metals, which wouldn't necessarily introduce better armor and weapon types (these should be balanced by weight and encumbrance vs damage or protection) but better metallurgy so blades are lighter and hold a better edge, and armors are lighter but protect a bit better. I feel like it's particularly clonky to say that plate armor is more advanced than leather or chain. They are different and offer different pros and cons and should be treated that way.
To me the Magic tree is egregiously the worst tech tree of them all. It offers very little support on its own and is particularly haphazard in its approach. And it's overly-synergized with the warfare tree. The enchanted weapons and armor mechanic is god awful. More city enchantments should be available through the Magic tree, especially those that might aid with things that buildings currently do (mitigate unrest, give food and production, growth.) The primary route of gaining more essence should be through the magic tree, and it should be easier to gain more essence. My Conclaves should be nigh bursting with magic. Maybe the only types of weapons and armors that can be player enchanted are created only with Crystals (Crystal Weapons and Armors); any found items which are imbued with magicks are considered Artifacts, and cannot be created by the current system.
Anyway, all in all I consider the tech trees a mess.