I'd like to add the following to the idea of ship designs. As you progress through the tech tree, the part's required capacity is gradually lowered, which means you can put more parts on a ship. My idea would be to allow you to build a chain of your own ships, so you'd have <shipname> M1 -> <shipname> M2 -> etc. for something you design by yourself.

The next mark of the ship should become available once it can be built, which automatically removes the old mark from the build list. There is a small problem with this of course, you would not necessarily get the M2 ship if you develop better lasers (i.e. lasers which take less capacity), because that M2 ship is designed with an extra shield, which still may take up (even with the better lasers), just one cap point too many. So depending on how you designed it, you may have to develop in the tech tree in a particular way, if you want a new mark ship a bit sooner.

However, I think it's still preferable to have a chain, that removes obsolete designs automatically, even if the self-designed chain is not as dynamic as the in-game chains.

I haven't played multiplayer, so I'm not sure how everything works; but in single player, ships you design in one game show up in another. If this is true if multiplayer as well, you can design your ships in a single-player game between sessions and they should show up in your game.