I've been pondering your post here for a bit. Yeah, I do like where the Galactic Civilizations tech trees ended up with Twilight of the Arnor. There, you had three weapons tree branches (beam, missile, mass driver), with your Galactic alignment determining which tree had the really cool uber weapon, once you built a certain galactic achievement (Temple Of Neutrality for me).
I was thinking about how to implement charges, phalanxes, mongol archers, and such, and the 'horse' tree presented itself in my mind. Something like this
Animal Husbandry - Draft Animals (economy bonus) - mounts - mounted warfare - cavalry charge - armored mounts - warhorses (trained attack mounts)
Cavalry charge would allow you to move and attack in the same action. Charge would activate once you have moved one square. At that point, when you move another square (without attacking first), you would be allowed to attack whatever was in front of you at the end of that second move. Of course, there would be a bonus to your attack (say an additional 25-50% to attack strength). Mounted weapons (lances) would be a little less powerful in regular combat, however, as a tradeoff.
A branch off of this line would be mounted warfare - mounted archery (a la mounted Mongol archers, i.e. you can move & attack at same time).
The Warg tree would be a little different:
Domestication - Wolf Servants (scouts/attack dogs), Wargs. I'm envisioning a branch here: Ice Wargs and Black Wargs, with each Warg having a different bonus. Then Battle Wargs (trained to attack, providing a boost to attack strength, or having a knockdown/tackle ability). Warg archery would be another branch of course.
As for Missile weapons, these have a LOT of potential for breakdown. Slings (2 attack), Thrown Weapons (3 for 1 handed, 4 for 2 handed), Shortbows (5 attack), Longbows (6 attack), Robin Hood Men in Tights Bow - 3 attacks of strength 4 each, J/K btw 
, Crossbows, Trebuchets, and finally Catapults. Also, ranges should vary based on the weapon (say range 3 for the sling, 4 for 1 handed thrown, 5 for 2 handed thrown (spears), 8 for shortbow, 10 for longbow, 12 for trebuchet, 15 for catapult, as examples.
Stepping back from that example, we sort of have the 'basic miniaturization/advanced miniaturization' sort of tree implemented in a couple of spots already. Arcane Mastery and Advanced Farming, each provides a % boost for every level you research, and apparently you can have as many levels in these techs as you want. Some of the Civilization tree also has increasing bonuses to Gold or mining. Right now, it just isn't as obvious.
As for the Magic tree, I think as you pointed out that there is a lot of potential here. As an example, teleport could be broken down (Teleport I works for 4 or less units, Teleport II for 8 or less, Teleport III allows the full 12, Teleport IV makes teleport cheaper).
