A way to have overlays that you can put on ships would be cool. Could just have a csv file where you can put overlay options in for each ship type, and if any are present for that particular ship there would be a drop down or something on the refit screen with the options. It could just use normal blending to blend the overlay layer in.
Even if the base game didn't include any overlays for the ships modders could create overlay packs for all the default ships pretty easily. It could be used for paint jobs (something as simple as a semi-transparent hue shifted duplicate of a ship could work as a paint job) or for adding logos to ships.
-edit- Just for fun, a paint job overlay for a Medusa. Just to show how easy it could be to make custom ones (only took me a minute or two).
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