Well. If you're looking at them as breeding prospects, you'd probably want the nicer colored one. But let's say they're both geldings... if I could get just as much quality from a horse that was the color of dirt, I would not bother paying extra cash just to be able to make people feel jealous when I trot by.
However, other people do
like when others oggle their shiny ponies, therefore, as breeding prospects, the nicer colored one is better if you plan on selling the offspring- since they're both quality horses, the offspring will most likely be quality, therefore they should sell at a good price anyway.
I wouldn't take the color into account for the babies either, though, especially if I gelded the baby, but again, that's really just me.
So basically, I wouldn't pay extra for color unless I was looking to breed with the goal of selling the baby, because others do like color... Although I would never breed if the horse didn't have very good conformation and temperament, anyway. Lol, I feel like I'm going in circles... sorry.