This is where I must disagree.

The Clone wars is a very different kind of beast to the Rebellion against the Empire.

The Empire in the OT are a monolithic despotic government.

They don't need markings on their ships (I don't like the blue TIEs for this reason).

The Feds and the Reps are opposing teams who at the height of their powers almost match each other.

Essentially both sides are the Rebellion but with something more like the resources of the Empire.

It makes sense they would draw attention to which side they were on by using colour.

In AOTC both side's ships should look clean and fresh too because they have effectively just come of the production line.

In ROTS both sides should look more worn down and patched up (more like the Rebels).

When the Empire takes over all the colour should drain out of the Star Wars galaxy.

Only the rusty hotrodded rebels with their tatty stripes echo the age of the PT.