Thinking about how ships can still be manufactured with D-mods present, I started to wonder whether in fact even the "Pristine" version of ships were actually the best possible version of the ship.
Take overclocking as an example, even CPU's sold at the same speed, they can be overclocked differently; my i5-3570k was sold at 3.8GHz, but I have run it for 6 years at 4.3GHz (which isn't a good result comparatively), where others with the same CPU could push this to 4.5GHz or higher. Not all CPU's are manufactured to exactly the same specification, due in part to impurities in the Silicon, hence we have the same template of the CPU binned into different markets; eg, my i5-3570k is the same silicon die as the i5-3770k but with the hyper-threading disabled and 2MB of it's 8MB of cache disabled.
In any case, the idea was to do the same with ships, some examples:
1) Orbital works with over 100% quality have a small chance to build a ship with a random High-Grade mod (eg Slightly more flux venting, better maintenance, etc)
2) You can use a similar function to "Restore" called something like "Overdrive". All ships in the game could have a "Quality Rating" which designates the ship quality of the Orbital Works that built that ship, and a hidden "True Quality" rating which is influenced by the "Quality Rating", but not tied to it. You then pay a rather hefty fee, something along the lines of the "Restore" cost, and the ship is buffed with one or more random High-Grade mods dependent on it's "True Quality" rating.
3) Another idea is to give more control to the player and allow them to adjust the stats directly on Refit screen dependent on the quality of the Orbital Works that built the ship (eg at 120% you can vary any basic ship stats by up to 20%). The difference here is that by increasing one stat, you will decrease another conversely by the same amount; ie if you increase your Armour by 10%, you decrease the maximum speed and Maneuverability by 10%. Perhaps to add a bit of variation to this so not all ships end up exactly the same, have the actual quality of the ship vary a little as in the second idea (maybe a little higher, maybe a little lower, but an average of whatever the orbital works building quality is).
I guess why I'm making these suggestions are that the ships themselves are the core of the game for me, but once I get to the stage that I have all the blueprints I want, I feel I lose a bit of that attachment to the ships themselves. It does accomplish the goal of making it a lot easier to deploy ships and worry less about losing them, but I'm not sure if this is necessarily a good thing....I guess I'm arguing for game experience vs game play.
With something like these High-grade mods, finding the perfect ship wouldn't end at having the blueprint, it will be an on-going process that will hopefully keep them interesting well into the late game.