The ship design system is powerful, but it could use some changes to make it more intuitive and easy to handle.
Firstly, even though this would add more potential clicks, the ability to group hull types easily (unless it's in and I've missed it) would help with 'design clutter'. For instance, I like to have a cheap, short range, slow colony ship for the early game, and colony ships of varying complexity to suit my needs without taking too much build time later in the game. Being able to limit the view in the shipyard to ship hulls by type, size, and user defined classifications would be very helpful in not having to pick through many designs for those of us who are quite thorough in their design specifications.
To be clear this isn't like the current ranking system as I'd seen on the design menu, but rather a filter system that the player can use to limit the number of designs they see to the ones best targeted to their needs.
More than that, I think it would be nice to, in the design menu, get a spy report on various factions, you see that your beam weapons are at this tech level, your shields are that tech level, and perhaps your spies have discovered that the terran faction is currently weak on chaffe. This would encourage players to build against their enemies weaknesses and add tactical depth. ...And it would encourage spies to outfox their enemies so as to possibly plant false information about an empires abilities, causing a player to waste resources building against a perceived weakness that does not match reality.
...For this reason, by the way, I think an enemies weapon capacities should not be seen easily on the overhead map as is current. I think it should be a research option (not taking research per se, but taking a certain amount of time to divine based on the current growth of technology, weighted by enemy technology and current technology owned by the investigating player)
For the above example, you faced off with an enemy in combat, and were destroyed, able to send only some rudimentary flight data back before your fleet was gone. This isn't much to go on, but your researchers are quite adept, so you are able to discover a potential range within 20 turns, which could trigger the possibility for enemy spies working against your empire to corrupt or manipulate the data. Of course, other engagements would make it easier to discover this, especially if those engagements are victories, etc.
And finally, I think it would be better if design changes could be done more easily 'on the fly'. That is, if you want to create a fighter with a great drive and limited weapons to get where he's going quickly only to refit later, it would be ideal if you could change that quickly, not needing to drag and drop parts, just selecting what you want to change as neatly as possible without needing to necessarily save the output as a new design (you may only want to use this ship once) before building it.
Alright, I have to go, if any of this is unclear, I'll return to it in the morning to clarify!