I get the backstory with the Y-Wings said they were once new and shiny but it was impractical to keep them that way, but I can't honestly claim to have ever thought something like that from watching the film. I definitely don't look at the Y-Wings and think it any more than I do about any of the other ships.

Now if we saw some shiney new Y-Wings in the PT and suddenly think 'oh look how run down they look by ANH' then thats good, it plants a little idea of history right before our eyes. But personally I think applying that logic to every ship won't work, and it would spoil that nice touch with the Y-Wings because it is no longer unique.

If we assume that all the ships in the OT are old, but the ones in the PT are new, then a close up of the Millenium Falcon in RotS could show it with a sleek metalic red exterior, which over the years was lost and by the time of the OT we are left with the heap of junk.

If the Republic has been around for a long time then let it look like it has. It can still look beautiful and old, just like I prefer old houses over new houses regardless of whether the old house is clean and shiney. The fact they weren't built perfect gives them more character. I would even say its not the colour that does the most harm, but the shapes of the PT ships, but colour is just the easier fix when editing.