Further weapon and armor specialization. Maybe one faction really likes bows and has limited melee options, maybe that same faction doesn't like metal at all and instead has better leather armor options (like with increased dodge). Another faction might be focused on spears and not have access to shields. Could pretty much flavor each faction with a specific weapon type and associated techs.

Some factions might favor certain tech trees, so much so that other trees might not even be viable and in fact empty or blocked out. Like a faction that doesn't have the warfare tree and has to rely entirely on exploration and magic for fighting and gearing up.

I'd like to see built in non-humans in some factions. Like right from the start one faction can build weak spiders and has future tech to unlock stronger spiders and techs to strengthen those spiders with special abilities or bonuses. Another faction might be similar with wolves. Heck maybe make a faction that doesn't have access to human soldiers at all (beyond the basic pioneer).

I really think each faction should be a different gameplay experience, with it's own tactics and quirks. Right now it's pretty much just picking which color you want to play.

I think you've missed the point of the question.  The question is:

What makes the Amarians different from the Ironeers?  What specific thing is it that Amarians are able to do better than everyone else?  What cultural conventions do they have that approach a problem differently?

I'll use some real life examples here.  Pardon the jump in eras, it's the differences I'm focusing on.

1) The Egyptians and to a lesser extent the Mayans were building HUGE buildings using complex engineering thousands of years before other cultures, despite being 'technologically backward' leaving behind some monuments to their skill that STILL have archaeologists trying to figure out exactly how they did it.  If it was easy, every culture in Africa/Europe/Asia would have these huge pyramid like structures, but in fact no Greek monument rivals the size of, say, the great Pyramid.  The Egyptians were expert builders.

2) The Japanese figured out how to fold steel to make very well designed swords during the same period that Europe had the sword.  The Japanese sword making technique was truly revolutionary, and it's taken material scientists some time to rival that technique.  Plus, their Samurai culture is a subject of fascination in it's own right.

3) The Mayans practiced human sacrifice extensively, because they believed doing so would increase their power.  While in reality all they did was kill a bunch of people, their whole culture believed this, and this influenced how they approached nature, their friends and enemies, etc.

4) North American Natives (Cherokee, etc.), for hundreds/thousands of years have focused on being 'one with the land', working within the limitations of their environment (i.e. no slash and burn agriculture) yet developing very intricate languages, beliefs and cultures that are different from each other.

5) The Spartans.  Amongst Greek states these are one of the most unique.  Males were separated from their parents at an early age to undergo years of martial combat training, a good percentage of which died in the process, to produce the best tactical warriors of their time.  They did so by conquering nearby kingdoms which were forced to provide for the "Warrior Elite" society, and also due to their 'selective breeding' practices had fewer warriors available, albiet very good ones.

I could go on here, but to put this back on track:

We aren't talking about ditching entire tech trees here.  What we are doing is formulating ideas for ADDITIONAL techs that will be plugged into the existing trees that make each Kingdom or Empire unique to itself.  As well as bonuses (although I don't think that bonuses by themselves sufficiently differentiate the cultures).

What unique technologies, structures, and society traits has Tarth adopted that make them different from the Amarians?  Or the Quendar?  Whom are the biggest builders?  Whom are most in tune with nature (and what does that do for them aside from a food bonus)?  Most comfortable with magic/have unique spells due to their focus? Are experts at metalworking?  Which culture utilizes constructs (Golems, etc.) extensively?  Are masters at combat/have unique tools of war that everyone else drools over?

I know some of you have your favorite Kingdoms and Empires.  Now's the time to voice what it is about them that attracts you to them, and what YOU think being in their shoes should entail.

Once we have some better ideas of what the various kingdoms and empires are about, then we can start formulating game mechanics to reflect these ideas.  But we need the ideas first. 

Pie-in-the-sky ideas ahead

1. I could see some special tech(s) that allow weapons and armor that are a cross between the current "regular" ones and the current "magical" ones. For example, Light Plate that uses both Metal and Crystal, but no Elementium. It would not be "legendary" but simply magically enhanced. Perhaps it wouldn't add any more Defense than regular Light Plate, but it wouldn't have a Dodge penalty, or something like that.

2. Another possibility is a tech or two that adds a few accessories that don't use crystal, like Vengeance Coating was before it was added in with the Arcane Weapons category.

3. Maybe a race could have a special ability that guarantees them one Horse/Warg resource tile (they can still find others as normal, if any exist). This could be a tech or a racial ability, but I'm thinking the best method would be to make it a city structure similar to the Beacon of Hope where you can only build one in your entire Kingdom/Empire. The structure would self-destruct if the city was captured.

4. Darklings are currently equivalent to one of your own troops equipped with a spear and armor of your choice that adds up to 3 Defense, yet they cost a whole lot more to maintain. Whether or not Stardock gives them a boost in a patch down the line, a cool racial ability would be to forge stronger ties than other races are capable of, allowing your people to teach them about some better weapons and armor. I can see this working in of two ways: 1) Darklings could be added to the Unit Designer and you could select between your own people and Darklings before equipping. Basically they would just have somewhat better base stats. 2) Additional pre-made Darkling units would become available on your Training list as they learn about new equipment from you (you would have to learn the equipment yourself first). Being the weakest of the allies the Empire can recruit, perhaps Darklings would not be able to learn about metal-using equipment (maybe Imperial Short Swords... but if so then for Option 2 they would have to add a metal cost in addition to the Gildar cost). For Kingdom, something similar might be done or perhaps they could learn to use Shrills as mounts.