I'd like for the devs in charge of character and BO customization programming to look at this video of phantasy star online 2's character creation because this is what you need to be aiming for down the road.
This is pretty close to what I would want STO's customization screen to look like. Instead of having most of the features on the same pages, the STO character customization window would change to a different customization screen everytime we selected a new feature to customize in the small, upper left menu (where the menu should be instead of strewn across the whole page). Alternatively, you could have 3-4 features on the same customization window, but that should be the maximum. Notice how the pop out menus for aesthetic options are much easier to manuever though than the single-column, top down lists we currently have for things like Klingon armor? Yeah, that's freaking awesome.
Let me know if guys and gals like this style of menus because I think it's pretty cool.