Regarding colorful ships in the Prequels, it's not so much that there is color, it's that it is too much.

Bingowings is right that the Rebels were differentiated from the Empire by their more colorful ships. But what bothers me is not fighters or smaller vessels having color-distinctive marking, it's the huge capital ships. Even the Rebel cruisers in RotJ were "bland" and gray(-ish). What distinguished them was their uniquely different design than the Star Destroyers; one was angular, industrial, aggressive looking ship. The cruiser was smoother, rounder, more organic looking.

And I think that the difference of having no or very little color helped with the issue of scale. Every time I watch the Battle of Coruscant in RotS, which has numerous other issues, I have the feeling I am looking at over-blown A-Wings. The ships don't have scale and look far too colorful and plastic for supposedly huge, tens of millions of tons of metal-clad warships.

The TPM as an example. Sure, it had some of the most colorful designs in the Naboo ships and the pod racers. But the Trade Federation designs, and the Republic diplomatic cruiser, while being color-distinctive still looked realistic. Their colors were more dull, muted. It was the overall coloration that distinguished them (the Trade Federation had brown and beige hues) rather than bright, flashy markings.

And the "donut ships" looked far better in TPM, even in AotC, than the flashy version in RotS. Due to it's distinctive design, not color markings.

Just my humble opinion. :)