Research Improvements
In general, I'd love to see both more cross-discipline results for the tech columns, and cross-column dependencies.  The cross-tree benefits would simply be fun, and the cross-column dependencies should help prevent the rush-to-the-top researching that happens currently.  Here are some quick ideas (probably not all good):
Bonuses from other paths in the tree could be things like:   
1. war paint - a battle item gained directly from diplomacy (described below)
 
Cooperation bonuses:  
1. researching enchantment and a specific spellbook might make an additional element-specific item available
 
In-tree requirements:  
1. adventure resource discovery requires some ruin delving after a certain level. Not only prevents straight to the top, but adds a level of risk to searching out the resources.  (Also please adopt more civ-like view of these - only seen by those who have researched high enough, but not just single spawns inside your domain)
2. a certain minimum armor level for a given weapon level (no legendary weapons with no armor at all), and vice versa - because that's just weird.
 
Cross-tree requirements:   
1. make the more legendary equipment in Warfare require civ production, and at least basic magical equipment researched.  
2. at least basic diplomacy before allowing larger squads (discoveries in organization & leadership)  
 
More specific ideas
I don't know if the capabilities for these sorts of things are built in or not, but I'd love to see things like:
spell: arcane bolt (known at startup, only available to sovereign)
damage: int/4 per bolt
number of bolts: 1 + # of shards (or level?)
cost: 1 + floor(bolts / 2) mana (this comes out to 1 mana per INT/2 damage, which seems fair)
Designed to give a somewhat-scaled offense to the sovereign that allows them some offense right from the beginning. Multiple bolts could be assigned to the same or different opponents (fire all at once or a quick stream).
 
auxiliary (additional to normal weapon) attack item: lance
required for selection: horse equiped
adds special ability: charge attack: 2.5 damage, must have moved at least 2 spaces, available 1x per combat
required for availability: mounted warfare (or something further?)
 
miscellaneous item: war paint
adds special ability: berserk attack: 1/combat attack for 2x damage, defense is halved for retaliation (or until next turn?)
required for availability: something in diplomacy (greater psychological understanding)