Hah, I feel your pain.
My usual game start involves about 5 mins of adding and removing name themes and adjusting % for names (I get like 12-15 themes). I hate this so I try not to start new games all the time.
The name picking should be tied to the % we can already set, that way we both get proper representation AND a way to alter it as we see fit.
You're not clear about which name themes you're having problems with, so I will point out that after you adjust all the name theme percentages for your empire, you can re-do your Commanders to get a whole new set with the chosen themes.
I truly wasn't aware of that.
In my united Earth games I use American, Chinese, Russian, French, Spanish, German, English, Indian, Protuguese, Japanese, Arabic, Turkish, Italian, Indonesian, Persian, Korean, Kenyan, Zulu, Jewish, Afrikaans names, roughly in this order (there is a distinct lack of african names to choose though).
I guess the way to go about is to pick names, select % and then go to Commanders and hit Auto rename?