I want to adjust the dominance values of all of my "natural" colored custom eyes to match the Maxis ones, however, I am not happy with how the Maxis ones are. Brown and Dark Blue are 1, making them equally dominant with each other, as are Grey, Green, and Light Blue because they all have a 2 - which I do not like because I think it's just not right. Is there any way to adjust the Maxis eyes? Where are the files for them located?

Okay then.

First off, that really wasn't much time to give us to respond. Patience is a virtue

To answer your question, find the texture overlays of the maxis eyes (C:\Program Files\EA GAMES\The Sims 2\TSData\Res\Catalog\Skins). Export those out into a new .package and change the genetic value there, and put it in your downloads folder. As for numbers you the game recognizes 0-4 with 1 being the most dominant (custom eyes); brown and blue 1; light blue, grey, and green 2. 3 and 4 are very recessive numbers so I'm not sure it will work the way you want, but rearrange and test to your heart's content.