WARNING: Massive Idea Dumping Ahead
One thing that I don’t like about the current model is how the Civilization tree is currently the only way to produce significant amounts of resources and research. I like how the Adventuring and Diplomacy can be used to accumulate gildar and materials, but I think this capacity could be expanded. I think that you should be able to support an army without significant Civ investment if you have that investment in other trees. In addition, the Civ tree is practically necessary for research. Again, Diplo and Adventuring can accumulate research, through tech trading and those caches of ancient knowledge (which there need to be more of).
One of the questions that has come up pretty often here is: how can small players fight big players? I think the answer is champions. Champions are tiny, concentrated packets of awesomeness. I think that all branches of the tech tree should have champions. Adventuring/Warfare of course have their combat-oriented heroes. Already in the game there are merchants, scholars, administrators, royalty, and so on. However, they become almost useless mid game because unlike combat champions, they don’t level. Even on turn 100, that merchant is still making 2 gildar a turn, while the combat hero is off killing dragons. I think that somehow performing their duties should give them xp and that their key abilities (making research/gildar/whatever) should be tied to their stats, like charisma for merchants and intelligence for scholars. That way late game you have some extremely valuable professionals. In addition, I think there should be a diplomatic hero type, maybe royalty or else a new type, who runs on Charisma, gains experience from making negotiations, and gives a bonus to diplomacy. To beef up the Adventuring tech tree, you could add techs that unlock tiers of experience (ex. 1-5, 6-10, 11-15), and perhaps a late-game repeatable tech that, on completion, spawns a random moderately strong champion at the gates of your capital and asks to join you (maybe for a fee, maybe not).
For the Magic tree, it has two great flaws: First, that it has to divide content between arcane research and technological magical research, and second that almost everything it does is for the benefit of a single champion, your sovereign. The way to solve the first problem is to make the magic tree do something unique and valuable (more magic items is a good step), and the way to emphasize the second is to make investing essence in champions more appealing, and creating wider opportunities for magic outside of combat.
The combat system right now needs more rocks-paper-scissors. It should be constructed in such a way that some units are inherently better at fighting other types of units. For example, when fighting a dragon, it should make more sense to bring a few good adventurers than an army. Perhaps the dragon has a large AOE low-damage armor-penetrating breath attack that will not faze high-hp champions, but will wipe even the largest groups of low-hp soldiers off the board.
One of the foundations of the fantasy genre in general and also Elemental in specific is that the world is untamed and has many dangers hiding in it. The betas have done a pretty good job creating this feel, but there is still more that can be done. I think that large areas of land should remain untamed even into the late game, and that the game should discourage and even prevent development of some wild areas, through powerful monster attacks, uninhabitable/useless land, and large patches where there are no or very few resources. This will prevent the game from feeling like one big developed chunk (like it does in late game Civ) and allow interactions between multiple players and monsters in the wilderness, and space for quests.
Finally, an idea I stole from Sword of the Stars. As called in that game, “Grand Menaces”. Late game, perhaps after one of the high end adventuring techs or quests that note that they “awaken imprisoned beings”, the world gets a small chance to spawn powerful monsters that roam around the countryside destroying cities and probably require special tactics to defeat. They should be so powerful that hostile players should seriously consider teaming up to take them down. I think this would seriously add to the epicness of the game.