First of all I want to stay that I appreciate what Stardock has done, because I LOVE these types of games!  Sorry, this a bit long....

First of all for the tactical improvements:

1)  Right now the game is pretty much "My stick is bigger than yours, I win."  Which is fine, but why have tactical combat if you are very limited tacticaly? 

The main reason for this is the weapon and unit design system.  The tactical benefits of equipment is either too low, or non existent.  Take the spear for example.... a weapon that was used for almost 400,000 years of human history because of its tactical advantage, is uselless after the early game.

The most important factors to choosing weapons now is damage, and cost. 

My suggestion is to change the weapons system.  Instead of just getting better weapons, you get a better class of weapon.  The classes would be something like: spears, ranged weapons, swords, axes, and blunt weapons. 

Secondly give each class of weapon a tactical bonus.

Spear:  first strike, bonus versus calvary

Blunt weapons:  bonus vs. armor and/or each attack reduces targets armor value by a certain amount in addition to doing damage

Swords:  good blance between damage, and speed

Axes:  High damage, low speed, and maybe have some bonus against shields

Ranged weapons:  range (obiously)

Lastly, for very weak weapons like dagger that are USELESS!!!  If you make a secondary weapon attribute for weak weapons, and then you can equip it to say.... your archers (ie units can have 1 primary weapon 1 secondary).  These weapons are no longer useless, which makes designing units more important, and increases the tactical depth of the game.

2 handed vs 1 handed - right now the attack bonuse from 2 handed weapons far outweights the shield bonus form one handed weapons + shield (in my opinion)  since if you are smart.... in most cases you can always hit the AI first. 

Give additional bonus to the shield.  Maybe something like % depending on shield size to avoid ranged attacks.  I know that right now shields give a dodge bonus, but the benefits are marginal in my opinion.  Also maybe give a special ability to shield carrying units, like shield wall.  For a certain amount of action points you can increase the defense of a unit for 1 turn.

I mentioned earlier about having a secondary weapon.  This can be used to make dual weapon units which would make both weak weapons, and one handed weapons more tactically important.  Plus it might give some sort of bonus or special attack to units.

2)  Horse/wargs.... no real tactical advantage.  Only movement bonus, but movement per cost wise you can make infantry as fast as horsemen by adding extra equipment for almost the same cost.... tactically the difference is marginal (in my opinion)...

Add some bonuses/abilities to horses/wargs

Charge:  mounted units do more damage to unmounted units

Harass:  a special attack that allows mounted units to use all thier action points to do a non-counterable attack (counterd only by units with first strike ability) and retreat

Also you can make horse archers with long bows... first of all that`s ridiculous.   If mounted units were only allowed use the short bows ----> short bow doesn`t become obsolete ---> unit design becomes more important ---> tactical depth increases

3)  This is mostly hypothetical, since I`m not 100% sure how this part of the game works.  Unit level`s biggest advantage seems to be health (I could be wrong, some one please verify that unit's level increase health), I haven't noticed any other tactical advatage.  This rather annoying....

For example, I had a platoon (12 units) of veteran longbowmen doing 1-4 damage 50% of the time.  I don't remember how much health a veteran platoon has (I think its like 200 or so depending on your equipment) but can you imagine how long a battle would take with VETERAN PLATOON VS VETERAN PLATOON!!!!!!!!!!!!  I haven't tried all combinations so maybe its just a bug, and not the system itself.....

Best way to solve this problem is to remove the generic increase health per level, and just increase attack and defense bonus.  Also per every level your unit gains 1 tactics slot.  So veteran unit would have 3 tactics slots.  You can use the package system like the ranger, scout, messenger etc.... have the units level determine how many of these the unit can carry. 

*Edit* Of course because unit design and unit production is seperate (you can't design veteran units, only produce them).  This a a bit tricky.... maybe make it into a selectable bonus when you click on the button.

Also add a bunch of bonus, and special ability packages.  Have the health increase one of these packages.... and reduce the price of the bonuses since you now have a limit.  This would limit the health vs damage problem in later games that I encountered.

Some package ideas that I have:

Combat Engineer:  Allows unit to fortify (not every unit should have this ability I think.... it would make making a diverse army more tactically important.)

Different Terrain Bonuses:  Alows unit to specialize in a certain terain giving them additional defense bonus/stealth while utilizing that terrain (this can have both strategic and tactical uses)

Combat Surgeon:  I know there is a package that allows you to heal yourself, but I don't think (maybe I`m wrong) that it effects all units in your army..... if not have one that can heal other units.

Poison:  Gives units additional poison damage.  Only unit that can do poison damage now is the black widow spider I think... why not expand this.

Different Moral bonuses/abilities:  I think there is moral in the game now.  I haven't noticed because it seems to serve no purpose.... maybe I`m wrong.

Special attacks:  You can get pretty creative with this...... if you want some good ideas play Age of Wonders, or Age of Wonders 2.

Now for the Strategic Part of it....

1)  Most of the special resources have no special purpose that I noticed and some resources are poorly tied into the tech tree

Basically my suggestion:  Controling Iron, or Elementium, etc should let you produce better weapons and armor.  Controling different food resource could have better bounuses not just more food.  For example if you have a Tavern, or a Inn in your city you can turn the different types of food into differnt types of booze.  Increasing the effects of those buildings.  Controling material resources, will improve the effects of your construction/material buildings.  Increasing the bonus to construction speed, reducing cost, etc. 

Furthermore, I think that what resources you control should have a greater impact on what research is available to you, and what you research should have a greater impact on what resources you can use.  Many of the games resources you can use straight from the start with no research pre-requisite.  For special resources I think there should be a prerequisite, and then once you get that research it makes other research options linked to that resource more likely.

For example..... you need to have a higher level of mining to mine Iron.  Once you get that research, it makes Iron weapons, Iron armor research more likely to come up.  Which in turn allows you to make units with improved weapons and armor.  I think everything should be tied together.

Also I mentioned earlier about adding poison ability.  This can be directly tied into owning a spider nest.

2)  Minor races are either too weak to be of any use or too powerful.  Each race (I haven`t tried them all, so only the ones I`ve tried) only allows for one unit to be built.  You can't customize this unit in any way.  This all seems imbalanced and pointless to me.

I think that when you gain a new minor race it should open up a new race tech tree branch, so you can research improvements for you special units.  Also instead of one generic unit.... you gain a new base unit option for that race in the unit design, with different options depending on what type of unit it is.  Special abilities for spiders, and the elemantal insect looking things (forgot what they are called).  Weapons and armor for ogers, and darklings.

One a final note:  I admited previously that I don`t 100% compeletly understand the game mechanics yet.  So if I have something completely backwards please let me know.  These are just my observations so far.