A few ideas to make the other tech trees more useful/interesting
Diplo tree-
Make the creatures made available by this tree more interesting. Problem is that the creatures made available are generally not worth the price of admission. I'll research up to dragons just because they're cool, but if I want to win the game then I'm going to just go up the war tree.
A couple problems/potential solutions-
1) When you unlock each one you can only build in one city, the one that pop's the associated resource. Which tech should I pick, one that lets me train powerful units in every city, or one that lets me train powerful units in one city? Not much of a choice. Solution- give us a building (say for level three cities) that lets us train these units in any city provided we have the resource somewhere in our empire.
2) The early allies are not very strong. Dragons are awesome. But the spiders, the shrill, and the drath are usually not as good as equivalent normal soldiers. Solution- make all the special allies much more powerful, and then nerf by only allowing a limited number per resource. For instance, perhaps the drath are 2 x a powerful as a normal soldier, but you can only have 10 of them per drath village you control. Well you can bet I train my 10, what an awesome shock force, but beyond that I'm limited.
3) All of the allies are not very interesting. They're just boring. I can train one type of spider, ho hum. I can train one type of shill, yawn. I can train one type of dragon, boring! Make all these allies more interesting and customizable. Make we WANT to play a game where I go down the diplo tree to the exclusion of the war tree. Let me get ice dragons, fire dragons, death dragons, Gold dragons, etc. LET me ARMOR up my dragons with plate mail! Let give them magical items too. Make these bonuses unlock-able through further diplomacy tech. The dragons initially scoff at your suggestions that they wear you puny human made armor "our scales are all the protection we need" they reply. However, a gifted human smith spends a year with the dragon lord perfecting his craft and convinces her to allow him to craft armor for her children.
4) Re-implement minor factions (I haven't seen any for many many games) and give the dipol tree bonus with them. And then make these bonuses really useful. For instance big discounts at their shops of unique and powerful items, free powerful units from them every few turns, etc.
Magic Tree-
Right now magic is essentially three things: spell books, mana harvesting, magical equipment.
1)Magical equipment and crystals. Make these more interesting than just slightly improved versions of those available up the war tree. Take a page from your own book and make magical creatures that are construable in cities: golems, specters, etc. and make the same adjustments as stated for the diplo tree. Finally to make them all interesting put in a rock paper scissors mechanic between the creatures in the diplomacy tree, magical creatures and equipment, and normal human soldiers with catapults. Magical constructs and crystal blades are vulnerable to good old fashioned plate mail and massive rocks. The creatures of the wild however are vulnerable to the crystal enchantments within your golems. However, those dragons make mincemeat out of knights and catapults are generally useless if they're on fire from dragons breath. RPS may seem contrived and overused, but there is a reason its overused: it works as a good way to force different strategies.
2) Spell books (never quite understood why their in this tech tree and not something you have to devote arcane research to discovering) But anyway, they occur very early in the tree and only a couple are really useful. Based upon the lore of the game we should want to specialize in one or two (the one or two we have shards for). Make this possible, make them all useful and dramatically increase the benfits to having shards associated with them. MAKE THESE MORE POWERFUL THAN THE BOOKS YOU CAN START THE GAME WITH! Then incorporate higher level books further down the research tree in order to unlock even more power. Don't just let me research the fire book as my third tech and be done with Magic for the rest of the game.
3) Mana harvesting, probably the only reason I go down this tree currently, and I can pull in all the needed techs researching magic about 5 times. No need for anything beyond that. Two improvements, make mana more dear by making permanent enchanments (especially city buffs) more powerful, I'm sitting at turn 138 in a game and have 756 mana in reserve. Mana is not a pressing concern right now. Second improvement, make a longer string of mana enhancing improvements. Right now there are essentially two shard harvesting and shard mastery. Once you have these you're done. Give us a few more that also give boosts.