I have some ideas about the further changing of e-civ tree (case of Pro and Team games):
1) Reduce the cost of wood, food and money gathering, for productive work of resource-mining villages. Big gathering buildings (starting with Cutiing Area) should be increased in cost but also have increased productivity.
2) The differences between low- and top-level of Strategic resources smelters should be greatly reduced; now we have 4 times more common productivity of strategic resources with the introducing of next level of smelters (e.g. IronFactory have productivity of all 3 IronSmith). I suggest to reduce this difference, because the lack of single science have very dramatic effect...
3) Advanced Strategic resource's Smelters should be available MUCH earlier in the game. In the Last Pro4 game I don't even discover IronFactory - let's remember, game finished at the 72th turn.

Also I suggest to introduce additional level of Bronze and possible Oil smelters and to balance its productivity to the Iron smelters - Iron output should be less than others.
4) Remove all useless or rare-used resources like Dragons and MemorialOfStupidity. Also I suggest to analyze the tree of knowledge for reducing the number of resources. E.g. it's very easy to completely wipe RaceHorse from the game.
5) Introduce "colonization" level of main types of buildings (like food, money, wood and stone buildings) with the reduced Construction cost and increased Productivity. But give him high resource cost - possibly Strategic resources...
6) For the economic-military balance I suggest to significally reduce "bonus city percents" for industrial buildings and increase (or add) these percents to the military buildings. Reduce the cost of military buildings.
7) Speed of equipment should be significanty reduced. As maximum I suggest speed 3 (totally 5) - for non-combat equipment like ScoutHorse (AKA Pegasus).
8) Range of fire for ranged weapons should be reduced; and limited by e.g. 4 - range of fight of hand-to-hand cavalry. Exception: immobile city defencive weapons.
9) Cost of war-machines should be increased.
10) Infantry battle orders should be more defencive than offencive.
11) Cost of terraforming and off-city consatructions should be increased. Roads included. Earth road should costs at least 500 points - so it should be constructed for moving purposes only.
12) Production of money buildings should be raised, but money-cost of economical and science building should be increased. This is the ecenomy-war belance action.
13) Balance the weights of weapons and armor; most or armors are lighter than weapons. Possibly we need to introduce additional sorts of armor - lighter or heavier than usual armor.

14) Ranged weapons should be produced in two-step process: e.g. first we need to produce Ammunition, weapons should be produced from Ammunition. It's quite simple in realization for modern weapons starting from Bronze but in the StoneAge there are problems...

It's additional balance between Hand-to-hand and Ranged weapons.