Alternative Character Interpretation: Your lizardfolk ambassador claims to be a champion of liberty and free thought, but a few event decisions like banning smoking, limiting the amount of children imps are allowed to have, and censoring scientific publications whose results her race considers embarrassing reveals she's just as hypocritical and self-serving as everyone else on the council.
Catherine, on the surface a champion for women's rights and having a Freudian Excuse for her misandry. Then you find out she was always a sexist jerkass toward men, treating them horribly under her rule, and realize that the male-led rebellion that kicked her out of power was probably not undeserved.
Broken Base: The game touches on many political issues and although it does handle it with neutrality, any debate between players can quickly turn ugly.
Game Breaker: Put a large enough squadron of Warlocks in the hands of a skilled player, and add a bit of support from, say, Shamans, and they can quickly undermine almost any opposing force. Meet the Beetles can make Hunters, Devastators, Armors or even Bomber Balloons completely useless for an astonishing 88 seconds (barring the use of Cleansing Charge). Death From Above deals massive damage to enemies if they bear the full brunt of it, and the Shaman's Cripple ability can hold even heavy units in place for 8 seconds, more than enough time to take multiple Death From Above barrages and utterly razing their health.
The Zeppelin is primarily a support unit, but its Mustard Gas ability can quickly wear down Armors, Hunters or Devastators, and obliterates groups of lighter units like Troopers, Grenadiers and Shamans en-masse. In a game where Zerg Rush is a viable and often-used tactic, Mustard Gas is pretty much the go-to counter for it.
Awesome Moments: Any time the player wins a near-hopeless battle, usually with copious amounts of draconic firepower.
Moral Event Horizon: The events surrounding Harrowdale. Namely the undead deciding that genocide was a perfectly reasonable solution to the "sins" of the libertine elven community. Even Edmund, as racist, self-absorbed and arrogant as he is, was appalled at what happened.
Some of the race-specific policies you can enact are rather horrific. The undead want to enslave and mark all nonbelievers and take away their first-born sons as slave labor. The dwarves want to institute a national smoking program culminating in mandatory smoking lessons in schools (that, notably, reduces your population). The imps simply want to build a humongous bomb... whose main component comes from elvish remains (and which, again, reduces your population, implied to be as a result of fallout from the bomb).
Is sacrificing your subjects or wife for power not horrific?
Narm: Quite a lot of dialogue in Dragon Commander comes across as being written for writing, as opposed to speaking. It has the feel of dialogue from a book, and a somewhat stylized one at that.
That One Attack: Meet The Beetles, the bane of heavy units. It's difficult not to scream in frustration when your impressive force of Hunters, Armors, Devastators or Bomber Balloons 'poink's into ladybugs one after the other, allowing the enemy Troopers to march right past them and ninja your base...or worse, charge into them and blow them up. At least your Warlocks get it too.
Uncanny Valley: Oddly, the Undead mostly manage to avoid this. It's a little odd seeing their skeletal faces contort as they speak as it would if they were flesh and blood, though. Ophelia may fall into this if you have the imps stitch a bunch of donated flesh over her her new golden body, depending upon personal preference (the resulting model is more-or-less identical to the "human" one.)
The Woobie: Ophelia. She has a disease eating at her body even after she became undead, the bulk of her own populace has no interest in helping her feeling that she deserved that for not being a complete religious fundamentalist in life.
Scarlett before she comes out of the closet. It's clear she's hiding something major, and that something's eating her up inside something fierce, and judging by her dialogue she hasn't had the easiest time with her sexuality.