Seems that the most 'loved' tech trees are Civ and Warfare. Which makes sense, to a degree - but I'd love for the other three to get some loving, too.
Adventure - let us add to our produceable (new word!) units by recruiting new minions (IE, recruit a pack of wolves, and be able to produce/upgrade wolves as a base unit); let us interact on a deeper level with NPCs (put out bounties on bandits, or on enemies, or on supplies. Get mercenaries)
Magic - Customize each spell, or enhance spells overall. Maybe let one book or another get some bonus, like fire magic doing extra damage over time, or restoration magic also buffing the recipient. Also, it'd be nice if special powers were 'tied' to this tree, letting us research how to, say, let our knights attack with a flaming sword strike, or teach units how to make a force shield.
Diplomacy - Interactions on a deeper level with the whole world. To me, diplomacy means more than just talking - diplomacy is politics, spies, etc. So on that vein, diplomacy techs would include espionage, as well as dealings with the people in our cities.
But mostly, what I would absolutely kill to see...
Is cities having more interactions than just producing and manipulating resources. Give us cities teeming with nobles, both self-serving and faction-serving, guilds that act on their own (wouldn't it be nice to start a war with someone, and find that their cities are crippled from the inside out by guilds allied with your own?), greedy merchants, etc. Let each city be UNIQUE and something special, rather than something normal and...well, bland.