It would be kind of fun. Have an option to upload your ship just before the first boss battle and let people fight against it on their runs.
It might not be as good as you are with it (AI RNG herpa-derp and all that), but god it'd make a lot of end battles harder. Maybe pick from a list at the beginning of the run of one of the top 100 run-ending ships. Or just a random pick from any uploaded ship that did beat all three stages of the boss, and give them badass points for ending runs afterwards. For, ummm, points. That are badass.
It'd make pure sense plot-wise (only you know the design layout of the big bad, and have to confront them with that knowledge eventually).
You'd know what you're fighting, so could design around it, but the top 100 would be pretty badass anyway. Or just the "only just made it, RNG is my bitch" ships. There'd be a heap of variety, and you could look at the plans whenever you wanted. Such a variety of challenges, you'd sort of do runs just to see if you could design around a never ending series of end-game challenges.
The evil ion. Oh, the Zoltanity!
ps. Does anyone else think that flak I is just an overcosted burst laser? Even a two shot burst is usually better than three flak pebbles. Most 2 or three shot weapons are really, even chargers or chain equivalents. Flak I just isn't very good, unless there's absolutely nothing better at around 2-3 power bars available to you. Anything really. Missiles, beams, ions, bombs included. Flak II is a totally different story though.