Raven - I commend you for your dedication towards creating customized races complete with backstory (in your head or otherwise) that feel at least as complete as the official races or factions included in games.
But the fact of the matter is, you are in the minority. Sure, I play using custom races/factions more often than I play straight-up unmodified stock factions in games, but I'm still strongly in favor of fleshing out the stock factions and leave more customization features for expansions and the like. My reasons are these:
1) I, and probably most people, would usually use stock races/factions as templates for custom races instead of building them from the ground up. The better developed, varied and flavorful the stock factions, the easier and more rewarding that practice is.
2) This is the biggest reason: my opponents. I don't often play multiplier at all, in any type of game, and I'm less likely to in a TBS. Therefore, my opponents are pretty much always AI. No matter how high your opinion of Brad or the rest of the Stardock team, there is no way the AIs will work as well for some random custom faction as they will for the stock factions; and I am a big fan of playing against factions with personalities that differ based on their story and background - it makes the world feel alive.
In GalCiv II, I probably played as a customized faction (including minor modifications to a stock faction) 75% of the time, maybe more. On the other hand, all of my opponents were always stock factions. Who my opponents are, how they behave, what they do, how flavorful and diverse they are just as important to me as the faction that I'm playing as. I never played against custom factions because it just wasn't as fun; the AI (strategy and personality) was built with the stock races and mind. Tacking the AIs onto Random Custom Race #82 is fine, it works, but it is an inferior experience.
If the stock races/factions suffer in order to give me a little more customization, I'll get bored faster because the world I'm playing in just won't feel as alive.
3) There will still be customization; we have customization already this early in the beta and I bet (and hope) it is expanded on before release. It's not massive, it probably won't allow you to create a new faction that plays completely differently than any of the stock factions, but it'll still provide variation to keep things interesting until Stardock can add in more customization or serious modders start produces high quality custom factions through regular modding. To be honest, I can't imagine myself ever downloading someone else's custom race that was made using pre-game custom race/faction tools. The sort of custom races I would download are the sort that would probably require genuine modding anyways.
4) Customization can be added in later. What matters in the short term after release is that the game is flavorful, engaging and developed enough that reviewers can't fault it and that people feel invested in the game world once they start playing. To that end, the stock factions should feel real, they each need to provide a meaningfully different way of playing the game, and they each need to provide different and varied challenges to the player when encountered as computer players. In GC II, if I will play very differently depending on who starts near me - if the Drengin are my neighbors, I will make sure not to put off military technology and ship building, while if my nearest neighbors are the Korx I'll probably prioritize my economy.
Customization is indeed very important to longevity, but if the core game feels incomplete or bland, then not enough people will stick around long enough for such longevity to really matter. On the other hand, if the core game is rich enough that the playerbase remains large for a reasonable amount of time, that gives Stardock the opportunity to release further customization options as part of an expansion and thus get the longevity we all hope Elemental will have.
Sacrificing the short-term success for the sake of longevity will result in neither. If one needs to be sacrificed for the other, extreme customization should give way to ensuring the short-term success. Because if the game is successful, the longevity can be dealt with later. If all the bits and pieces are there for people to turn the game into exactly what they want, but the game isn't rich or developed enough that people really get into it, then that potential won't be realized.
Sorry for the long rant... It's 4 AM and I'm procrastinating!