A long time ago i suggested to use a set of ship sprites each decorated for a specific faction. This is how i imagined it to work:
- each ship hull file contains a list of usable sprites. Say, 1-2 for each faction and some extra for player`s choice (with some non-faction decorations). Each sprite has a short name near the file source (TriTachyon, Hierarchy etc.).
- each sprite MUST retain all weapon, drive and system positions.
- in variant file a string should be present that specifies what sprite this particular variant is using.
- a refit screen contains a button that opens up a list of available sprites for this ship. There are icons for each sprite and short names for ease of choosing.
This way the game will always use one sprite for the ship and will apply all damage decals directly onto it.
Now just imagine how many new mods this simple solution will give birth to! And how it will improve the quality of all existing ones.
Devs can release an example of one of their ships and allow the community to finish all the other sprites for all factions. Make some kind of competition and pick the most appealing ones

The only drawbacks i see here for us modders are huge amounts of graphical work and probably significant increase in mods` sizes.
Here is an example of some sprites for the same ship:

EDITED:
just accounted all ship sprites in my mod and the size in MBs that they are using. It turned out that 100+ ships take just 6mb of space. So if i make 4 more sprites for each ship (4 factions + without decals/pirated) this will be 6 + 6*4 = 30 mb.
Current size of the mod is 12 mb (due to lots of weapons, some sounds and text files). So these 12 mbs + 24 for the new sprites will be 36 mb. Not that much even if it triples the size of the mod.