If there is any idea and mentality in the Stardock offices concerning efficiency in focusing on things felt important and necessary, than I understand completely from your Independent perspective. However, I feel you are combining this "content-focus" with "game-lore design" for lack of better words, mentality to much together. Furthermore, I understand and love the faith in suggesting the modding community to come will up take the reins to create content, yet, imagine if the developers of Age of Wonders just scrapped all twelve unique races and said "Let's just have Elves and Dark Elves, let the modders create the Orcs, Humans, Frostlings, cetera." Comparing that example to this, it is exaggerated and broadened, but merely mean't as an example.
Thus, I feel you should keep the unnecessary lore-oriented races such as the Trog, Urxen, cetera and let them be part of the Fallen Genus, but be their own individual Species and have significantly different, yet similar strengths and weaknesses related to the original Fallen-Men.
One of my biggest concerns is that multiplayer games need to have an option to prevent user-made races and the "culture" factions be one of the regular permanent features. I'd hate enough to see peoples poor excuses for Avatar's and Michael Jackson's, but as actual races!? Michael's getting +1 Fertility!? *Shakes fist in the air* "Damn you Frogboy, damn you!"
Finally, I think you should seriously consider implementing what Master of Orion 3's modders found in the files, being their Ethos system. http://moo3.quicksilver.com/official/religion02.html
If we are to have our own factions between these two races, (please mix it up and include the other two!), than we need some sort of dynamic, say, "a clash of cultures" between factions. I haven't fleshed it out in my imagination, but factions whether they're paired Fallen to Men to each other wouldn't decide all, but be judged almost entirely on their strength and weakness choices will find themselves either more friendly or hostile to each other. The idea that on one end of the ethos-spectrum exists civilizations of Men and Fallen co-existing peacefully like blacks and whites in America sharing the same ideals that are primarily focused around material things, knowledge and class is possible. Yet, how absurd and truly alien this must be and is to co-existing Men and Fallen that place physical strength, ancestral beliefs and military traditions above all other aspects of their culture. Thus, you will find whether Fallen or Man, will when diplomatically dealing with each other or you have cities that share different factions with far different cultures, become great concerns and obstacles in your games.
Though Factions should without the players deliberate input and by natural world development, gain and lose their strengths and weaknesses unless they're not racial, but only cultural (factional). Natural world development being, if your faction of Fallen are the best miners in the game (+5) yet you haven't established a mine or quarry in first 50 turns, they'll lose 1 or 2 points off that strength. Factions populations that are hostile to each other are taken over, and their original faction still exists in the game, they'll act as if they're subjugated and worst, at war, just in the streets like guerrilla fighters. It will take large parts of your gildar revenue, large garrisons and dozens after dozens of turns to comform them to your culture. However, if their original faction died, whether friendly or hostile, they'll more easily lose their original traits and begin replacing theirs with yours.
I know that was a lot, but this Journal excited me lol.