Frogboy mentioned yesterday that tech trees are a bit of an issue that needs some focus. I'm thinking that the game simply doesn't need them at all.
Tech is really good if you are playing a SciFi game or a Civilisation-type game where you progress through different eras. But for a fantasy game it just gets in the way.
Consider the following:
The Civilisation, Warfare, and Diplomacy trees could all be moved to buildings that are unlocked at different city levels. Or are unlocked on events.
As an example, Town Halls unlock at level 3. Schools unlock at level 4. Want to build chain-armour troops? At level 4 you can build a blacksmith that will allow you to build chain-mail at that city. Want plate? After you have built a blacksmith you can then build an Armourer in the same city. And so on. Caravans could be built once you build a Merchant in a city. And treaties could be actioned once you have an Embassy.
Basically the city building takes the focus for these tech trees rather than specific research. This would make the game much more focussed on the game-world and provide a nice RPG feel to the development of your cities.
The Adventure tree could be handled through a mixture of counters and buildings. Kael mentioned that there is currently a spawn counter for monsters that is tied to the collective research in the Adventure tree. This could be tied to the collective size of cities instead. Notable locations and allowable quests could be tied to Adventurers Guild buildings. The level of heroes could dictate what level of quest or location they can enter.
As an example, You have a stack of heroes and units enter a level 3 notable location where you must fight a pack of wolves to get the reward. Only two of your heroes are level 3 or above so they are the only two that enter the tactical battle.
Once again, this would make the RPG element for specific heroes much more interesting.
This leaves the Magic tree. Magic and Science are not a good mix for a fantasy game and seem to be at odds with each other. Magic should be completely removed from the tech tree no matter what happens with the game.
Instead, each spell should have a percentage chance of appearing when it is time to research a spell - based on its level. As you research spells from a book you increase the percentage chance of having higher level spells appear. The cost to research high level spells is still expensive so even if you do get the option to research a powerful spell on the first turn you need to weigh up the amount of time it would take to research it. It may completely change the way you play the game because you may decide to research this particular spell and spam archivists rather than focussing on improving your troops.
New books could be unlocked via buildings or events.
As an example, you could build a Temple of Earth at a city you have an Earth shard which unlocks the Earth spell book. Building this also gives you a mana boost and you can build special Rock Golem units at this city because of it. The more temples of this Earth element you control, the higher the likelihood of accessing the higher level Earth spells.
This does three very important things for the game:
1. It makes the shards more important.
2. It makes the game-world more involving.
3. It adds a powerful incentive to play differently based on the spells that appear ready for research
So what becomes of Lost Libraries and Studies?
Technology can still play a role in the game - but a limited role. Science in a fantasy game should be more about discovering methods to make sharper weapons (a boost to attack values) or making stronger armour (boosting defence). It may unlock some weapons such as muskets or cross-bows but the standard weapons should come from the buildings in the cities.
As an example, your librarians could be focussed on 'Reinforced Skull Caps' which adds +1 armour to leather helms. The leather helms themselves are available once a city reaches level 2.
Science could also be about creating items for heroes.
Please feel free to comment. 
