Imperium/Civilization
This tree really just provides the supports necessary for any other tree to succeed, while it's fairly fleshed out I'd like to see it even more intertwined with your advances within other trees. The game already tracks what rank you are in each tree, would it be possible to have it unlock more powerful techs when two or more trees are at a certain level. In addition to the tech level requirement there should likely be specific breakthrough requirements as well.
Example: Iron reinforced Walls
Req:
10 Civ and Forges
10 Conquest and Fortresses
Or
Magic Reinforced Walls
Req:
10 Conquest and Fortresses
10 Magic and Enchantment Foundry
There are so many possibilities for enhanced structures that combine the powers of multiple trees, and it makes sense really. Why wouldn't the breakthroughs in various areas lead to more breakthroughs that take from both? This might fall under the category of new research rather than rediscovering old technology. Perhaps once every X turns you get the chance to choose from a list of techs your civilization qualifies for from this special tree.
Adventure
I understand the intent of this tree but I don't particularly care for the implementation. It is really cool to find ancient artifacts and dungeons but everything attached to the tree seems fairly trivial. Quests are rarely challenging or engaging and despite research into the heroes line I don't often see them showing up. There also needs to be a much larger variety in quests/rewards to make it viable.
The master quest should be more like the Grail from HoMM as in there is only one, or in this case 1 of each of the 5 pieces, and they are scattered all over the world, they shouldn't be anywhere near each other and assembling them should be a truly epic journey worthy of being a game ending event. Each piece should really be guarded quite well, residual power within the shards should draw all manner of powerful beings to them. In return for this obtaining a shard should also offer some bonuses while they are carried. Perhaps instead of just gathering 5 nameless pieces they act as artifacts while you carry them and only assemble once you have all 5. The more pieces you have the harder it becomes to stop you from acquiring more. Thus creating a situation where everyone might band together to stop you.
I noticed some people looking for ways to make champions more unique and this should probably be the tree to do it in. In addition to the current tech unlocking quests and drawing heroes to you, there should be a way to strengthen them within this tree. Passive bonuses similar to what exists in the conquest tree. There should be a way to add combat abilities to our champions as well, also through this tree. Ancient fighting techniques unearthed in the tombs you're raiding, it would go a long way to making this tree a lot more appealing and self sustainable.
While this tree may not mesh as well into the tech combining tree I mentioned earlier it could provide its own benefits to cities and such. Perhaps you find ancient building plans allowing you to construct a new more efficient magic foundry or forge. Discover the location of rare metals that you can create an alloy with iron so any metal armor and weapons you create are slightly enhanced. Discover sources of power that increase mana regeneration, or simply provide empire wide passive bonuses, once discovered all the world can see them and fight over them. The potential for this tree is amazing, it could add so much more to the game than it does now.
Warfare/Conquest
This tree is pretty straightforward and is much like the civilization tree in the ways it could add to the list of combined techs. It also cannot really function without the support of civ techs. Unit recruitment is massively expensive and needs substantial support from multiple upgraded cities to even begin to field something that resembles an army.
The warfare tree could benefit from advances in magic tech more so than it already does, via weapon and armor enhancements or personal enchantments. Perhaps there could be buildings that allow you to not only enchant armor and weapons but your soldiers as well. Ways to enhance/speed up training or lower the cost of recruitment via magical means.
The adventuring tree could add new training types as lost arts of war are recovered, formations that provide bonuses to multi-soldier units. Fighting techniques or special training that increase ability with certain weapon types or offer new combat abilities for tactical battles. These are rare and lost fighting arts well beyond what standard military training provides.
Magic
This tree is pretty barebones right now, I like the two current repeatable techs, especially the essence boosting one as it allows you to imbue a champion and have them be a semi decent caster from the getgo that can at least provide support with a few spells from the beginning. I believe I saw somewhere that custom item creation would be a feature of the full version, if not, it should replace the current techs that unlock the groups of minor magic items you equip troops with.
Instead have techs that allow you to design items similar to how we design our troops. Those items are limited in the enchantment they can hold based on how skilled you are at enchanting them. Perhaps a combination of your spell level and various tech levels of item enchantment in the magic tree. This could be further enhanced by the discoverable resources from the adventure tree. The base items available are defined by your advances in the warfare tree, higher quality items have a higher enchantment limit.
In addition to this, the magic tree should also offer research into specializing your spells more. Not only to do more damage but to add secondary effects. Say you specialize in frost, the first rank increases damage a bit, the second causes frost spells to have a chance of slowing the target, the third raises that chance, and the fourth gives a small chance to freeze as well. Since damage types are in the effects could be tied entirely to that damage type.
There could be research into spellbooks discovered via the adventuring tree as well as research into combining the schools of magic. Volcano is a current implementation I'd love to see more of, dominions 3 has many spells of this nature and could be a good place for inspiration for this, they've got a similar setup of mixed elemental spells.
Spell of mastery as a win condition is decent, I fear on larger maps the conditions will be too easy to meet and there might not be as much conflict required to actually gain control of one of each shard. Maybe scale the requirement up on larger maps to be a certain % of ALL magic shards on the map controlled with at least 1 of each. If this spell you're casting is going to end the game and control the world you should have to control a substantial portion of the magic in that world.
Diplomacy
This tree is practically empty currently and most of the techs are unlocking treaties that shouldn't really need to be researched to begin with. I like the diplomatic influence as a resource that raises your standing with people and think it's cool that you can trade for it. I'd like to see more ways in this tree to create this resource but also turn it into a diplomacy/espionage tree. Intelligence, spying, and sabotage are all integral parts of diplomacy and always have been.
I suggest a line that allows you to build units for these purposes, diplomats, spies, assassins, saboteurs, and even bandits to raid trade caravans but without your banner. They could be enhanced by magical abilities from the magic tree, skills and items found with adventuring, equipment from the military tree. Maybe even have them designable from the troop design but with a different base unit than a military soldier, somebody that can level up but only in their specific ability.
I'd also like to see more enhancements to the trade aspect, stronger caravans with armed guards (military), magically enhanced caravans that can travel faster and carry more (magic tree). Trade ships for overseas trade routes, hire privateers to raid enemy trade without your banner being involved.
Perhaps we could even have units that can work to convince cities to join our kingdom/empire. If you manage to infiltrate the city with enough units you can eventually start to sway the local government and overthrow the town in a rebellion. This would be a hit to relations with the enemy nation but nothing your diplomats shouldn't be able to handle
You are the master of diplomacy and espionage afterall.