I was part of the WoM beta, but I haven't commented here much because, well, I felt like every minute I spent on WoM was time I'll never get back.  I'm glad you guys have decided to give me Fallen Enchantress, though - it's already a substantially better game than WoM.  But then, I've had GavCiv and Fall from Heaven continually installed for years, so, there is that.

I do a lot of software design/testing, and I've worked on board game design as well, so I understand the tradeoffs involved in making changes to things - what else will it effect, how long will it take, that sort of thing.  Also, you're using an existing engine to build this thing, which necessarily imposes certain constraints.  That being said, I have some thoughts on the current beta:

First, cities and city building.

I don't understand why you have an arbitrary no-settlement area around existing cities.  You already constrain city building to a limited set of "fertile" squares - why add the extra constraint?  If the idea is to reduce city spamming, that's just as easy to do with the economy.  I strongly recommend you get rid of this altogether.  It adds nothing beneficial, and makes expansion more of a pain to plan.

On a related note - please god make a different tile for fertile squares.  Don't make me hover my mouse over them to see if they are fertile, and if I have the "display values on map" function turned on, for chrissakes don't make FOW hide the values.  Building cities is an important part of the game, and the current system makes it a pain.

You need to decide what the core parts of this game are - carving a civilization out of a dangerous wilderness is the vibe you're looking for here - right?  So then why are my borders pushing all the monsters away without me doing much?  Monsters should come after settlements, not run from them.  At this point, I can basically clear territory just by settling - it should be the other way around - I need to clear out the monsters before I settle, or the settlers gonna die.  The AI work you're doing might address this, but it's something that you should address.

I like outposts, I like resource harvesting.  I love the national pools for resources and materials.  But there are some things about cities and building which are very problematic at this point.

Second, city development.

What are you going for here?  Every part of a game should present interesting decisions.  And the process of developing your cities in the current version just doesn't.

What is the point of making me place all my city buildings on the map?  It adds nothing to my gameplay experience, it's artificially constrained by the fact that I can only place building next to other completed buildings (except for resource nodes, for some reason).  There is almost no economic or strategic benefits to how you build your city.  Essentially there are no limits to the number of buildings you can build, and placement of the buildings does barely anything.  SO WHY ARE YOU MAKING ME DO IT? 

Adding to this issue is the fact that the squares for adding city buildings are tiny and fiddly, the buildings themselves, while no doubt a lot of work to develop, are basically all just tiny boxes that get lost in the clutter, and the expanding cities look like... well, crap.  More squares, laid on top of the squares that make up the world, next to the square rivers and square forests... what is this, minecraft?

Also, the cities are only made up of the specialty buildings.  Where are the people, underground?

My proposal here is this.  Either a) get rid of the entire building placement business and just develop cities like you do in Civ, which is basically all you are currently doing here anyways or allow me to place the buildings anywhere in the cities ZOC, and give me incentives to place them in myself - for example - give me bonuses if several training buildings are placed together.  Production bonuses if production buildings are adjacent to resource nodes or forests.  This would also mean that you could specialize cities more - and give certain resource nodes several potential bonuses, making you think more about building placement and city development.  Plus, this makes you scatter buildings around an area, making it more challenging to defend against raiders and creatures and enemies. 

Third, the colors.

Good god, so many squares. Everything so grey, so horribly grey and washed-out.  And the ruler-straight roads...  You probably have limited resources to throw at this, but this game is ugly.  Colors are good.  Please throw out the Fallout 3 color palette and give me some interesting stuff.  But that is a lot of work, which you may want to spend on other stuff.  Still, it impacts my enjoyment considerably that I can barely stand to look at it.

Fourth, technology and units.

There should always be a reason to build a unit, and a situation where a unit is useful. The unit maker is good, because I can design units that meet my specific needs or resources. The other units, things like Mercenaries or Ogres - they need to either have the tech requirements removed, or  have it dropped way down.  To train Ogres, there is a resource requirement, a tech requirement (a very high one) AND a numerical limitation.  But at least it's fast, so it's not a total waste.  And the resulting Ogre is nowhere near as effective as a unit built with a similar tech level on the military side.  There should be only one of these requirements, ideally the resource one, and the special units should be more effective than a military unit of similar level, because they are more rare.  Limited numbers is OK, though, that's nicely thematic.

Fifth, movement.

Tactical and map movement does not have to be the same and you are artificially limiting tactics available in the tactical battles by making it the same.  I should be able to use light, fast troops to get around the edge of my enemies, attacking their archers or mages.  Cavalry should be even better at this.  Right now, there is no reason not to just clump up in the middle of the map and hammer away.

Pursuant to this, bonuses for attacking units from the rear or attacking units that have several of your own units adjacent to them would be very useful, and encourage tactical thinking/movement.

Additionally, the tactical maps need to be bigger - there is no space on them currently for complex tactics like hit and run or flanking attacks.

Sixth, Archers

Archers need a distance penalty - this business of firing across the map is garbage, and also discourages tactical movement/placing.  

Also, bows should either be slower than other weapons OR they should hit harder.  Historically bows are actually very fast weapons, but limited by ammunition supply and ineffectiveness against armor.

Seventh, Spears

Spears are not armor-piercing.  Most spears have also been 1-handed weapons, used with a shield.  In fact, unarmored spear and shield is probably the most common type of military equipment ever used.  Pikes are 2-handed, and are a totally different weapon, used for very different purposes.  It's good that spears are low on the tech tree, but they don't make much sense the way they are implemented here.  See next comment for more thoughts on this.

Eighth, Weapon types

 The whole idea of armor-piercing needs to be scrapped.  You already have several weapon types, crushing, piercing and slashing, I think.  Make certain types of armor more effective against certain weapon types, and let that serve to replace "armor-piercing". Make shields equally effective against all types of weapons to make them desirable.

I've got a few more thoughts as well, but that's probably enough for now.