I would start off by saying that I have high hopes for this game, what Stardock can't/wont do the modders will. I fully expect to be playing this game when I am 50.
Many things written below aren't my ideas; I am just adding my voice to the chorus in this case, raising the volume and adding my own distinctiveness.
Resources:
Food should be tradable, 1 food per turn for 20 turns for x money... If it is the rarest resource in the world it has real value; I may end up with lots of food and no crystal.... for example. Also helps people get over the whole caravan thing.
While you're at it make everything tradable. I may not have the racial aptitude to raise and train wargs or spiders but how about trading for already reared/trained ones.
Shops:
As mods are developed I expect to see tons of stuff at the shops. Diversity in shops, from one loc to another (quest shops = hot).
Catagorize shops, I already have thumb fatigue from scrolling through the shop list.
Very rare resources that yield superior kit in the linked city. unobtainium mines make your armor better in that city. Legendary plains horses make faster mounts... etc.
Spells:
Diversity in spells is great but so is parity in spells. If I end up with 12 water shards and no fire... you get my point, or points rather, as in shards...ok I'll stop.
Summoning items would be wonderful. A summon a simple sword that lasts for 1 or two turns would be fantastic for the early game. Remember to not use regular weapons as the summoned items as people will summon them the sell them 
.
A maintained strategic spell that modifies the weapon/armor/kit of the units built there. IE enchanted weapons for your troops.
A clear forest spell.
Tactical magic is really powerful... too powerful in my opinion. A caster with the mana tower and 40 int is unstoppable.
Weapons/armor:
The whole speed bonus for weapons....well on magic ones I go for it but movement speed needs to be addressed, perhaps use points as others suggest: 100 points to move a tile, 20 points to thrust with a dagger 1 time, that sort of thing.
Armor also needs a balance pass, master light/heavy... why did you even make the light?
I often think that games designed to be modded don't take full consideration of what modders do. Everyone wants their weapon/armor to be a bit special, more so than the default stuff that's in the game. Problem is when your damage scale for weapons is 2-20 and 1-15 for armor you end up with 1 single point added making a huge difference. I would balance the game for a very large scale, 1-100 or more. It allows us to have many unique weapons, armor, monsters, units, spells, etc. without spoiling the balance of the game just because we want our 8th level raging inferno spell to do more damage than the 4th level woosy inferno.
Tactical:
Flanking bonus/penalties.
Fatigue, would really mess with the guy that has 10 points of combat moves and 10 stamina.
Damage/resist types. I see from the .xmls that you had something in mind here, just didn't have time to implement it?
The "glass cannon" effect: A few things could mitigate it:
With your counter attach mechanism add another counter attack, when one side moves into a square adjacent to a mob that prompts a counter attack. It makes sense and it makes it harder to attack once, move back two wait for mobs to advance repeat.
Balance to make it so that you can rarely get killed or kill with one shot, so there is always at least, preferably more in "even" fights, two exchanges (attack, counter, attack, counter, attack, death) at least this much sword play.
A better combat speed system would also help.
Greater diversity in monsters (more below).
Monsters/units:
Randomize mob stats and the attacks they use i.e. normal trolls move two, but Urg the swift's swiftness is famous among his people and can move 4. In the same pack is dim the stupid and god only knows why he became a shaman. Wolves are fast, if they could move 4 turns a combat round they would seriously mess with the glass cannon. That rare wolf that happens to be a glass cannon himself would add a lot of fun to the fight.
Hide the monster stats from players; instead give players hints in the monster name for rare random exceptional (Urg the swift from above). I think I have seen one mob that can move 3... one of the quest mobs.
Tougher monsters. How about instead of 2 monster groups per "uninfluenced" tile late in the game we have one every 4 tiles and it is a bruiser. The current system creates lag, makes it stupid easy for humans to accumulate huge wealth and power, and makes it impossible for the AI to do anything outside their influence late in the game.
About this late game monster spawn....well its nuts, as you know. How about ignore global monster level and just spawn 1 mob for every 4-5 uninfluenced tiles and use global monster level to calculate the types/levels/group size of the monsters you spawn. Global monster lv + average hero level > lv 1 = average monster level. I fought one lv 11 monster and it was fun.
Variation in level up attributes: gaining nothing but hit points when leveling is meh.
Give different mounts different strengths. Wargs perhaps move through forests and swamps at their full speed while horses move at full speed through open, hills; something like that. Different classes of mounts; I modded myself rounceys, coursers and destriers.
Greater diversity in heroes talents, If I see yet another "adventurer" I am going to scream. I modded my heroes and histories and all but eliminated "adventurers". A sample of what I have now: knights, scouts, wizards, rangers, gladiators, etc. A few things I would like to do but cant..like make having a ranger or scout in the party move faster across rough terrain.
The dragon you get from the quest.... dragons fly, <movementtype> air</movementtype> exists switch him to that and change his moves to 6, he is a lot more fun that way. Would be awesome if you could turn him into a boat, ride him, (actually you can) but that has problems, not least of which is he can move a whole army when he should be able to bear aloft one hero not 10.
Make old units upgradable. There is no game play reason you can't only game mechanics. Game mechanics are ugly things, we players hate to see them. The lv10 peasant should be the grand elite battle hardened badasses of your army but some 15 year old with a long sword and plate armor can clean their clock. Any intelligent commander would give the bad ass kit to the bad asses first, 15 year olds last.
AI (the bad guys):
Less stupid, use boats, B E Aggressive, be more aggressive. This should be at the top of my list really.
In tactical...well everything pretty much always uses the same spells.
UI:
Display chosen unit path.
Highlight selected unit much better (hard to see in strat map).
Waypoints for chosen units (including caravans and their pending roads.
Hide things from left panel ribbon (guarded units for example)
Hot key grid overlay ( I don't want the grid on all the time but would like it for placing cities and that sort of thing)
Center on selected unit button
Right click to center to city/unit from left ribbon without deselecting current selected unit.
Does the road upgrade thing from the .xml files work? If so it should show up on the map. Would really like to have some control over where caravans place roads, driving through that uncontrolled forest is bad.
City:
City level up screen needs a display that shows what that city is producing, what resources are within say 5 tiles, and what upgrades have been chosen in the past. Better yet get rid of the level up choice screen and just put in 3 radio buttons so we can select (still apply the bonus at level up though). You could also have 3 auto balancing (totaling 100%) sliders that would be even better than radio buttons. I don't see any reason why we can't retask a city once the decision at level up is made.
Some sort of resources linking tool that doesn't involve a chain of houses so you get a 1x20 town. I always end up with unlinked resources from the various research revealing techs.
Buildable forts, guard towers, etc. That I can place along my trade routes, routes of ingress from other empires for attack, edge of my influence to guard my shards, etc. Small zone of influence associated with them, extended fog radius. How about if my caravan or other unit is attacked within sight range of my fort I can opt to send units stationed at the fort to assist the attacked unit. That would be a fun tactical trick. Caravan attacked, units from fort deployed but on tactical map the fort units show up on the other side of the attackers....can you stop the attackers before they destroy and loot your caravan?
Yeah some of this stuff doesn't belong in this thread but I got on a roll.
