I have a lot of issues with the game that probably can't be fixed (I consider the entire ship building/upgrade side of the game to be a major annoyance; suffice it to say I find it easier to design a new class every time I get a new weapon or engine rather than messing around with the buggy upgrade feature) but one issue that I think should be fixed concerns obsolete ship designs.
When you mark a design as obsolete, it disappears from the shipyard screen, but it does not disappear from many of the lists of ships that appear throughout the game. Obsolete designs still appear in the following places, severely cluttering up the menus and making upgrading and shipbuilding difficult:
1. When you choose to upgrade a ship to a new design (a process that really should be called refitting; you upgrade a design, but refit an existing ship; its confusing to refer to both processes as upgrading), obsolete designs appear on the list of choices, forcing you to scroll through every ship you've ever designed before you find the newest design.
2. Obsolete ship designs are selectable when you try to change military production on the colony list screen.
3. Also appearing under colonly list military production sections are earlier version of existing designs, which I simply don't understand at all. This is the upgrade bug I was referring to before. Its hard to explain, but people are bound to have noticed this. Let's say I design a "Terran Cruiser" with ion drives. I later get warp drives and select upgrade on the shipyard menu. I change out all the ion drives for warp drives. From that point forward, "Terran Cruiser" will appear twice on the military production screen and you have to look very carefully or else you will build Ion drive equipped ships rather than your newer Warp Drive ships. This kind of eliminates the entire point of the upgrade feature, as I mentioned above.
It would be nice if all military production and upgrade/refit screens reflected the list of ships shown in the shipyard. Obsolete designs and earlier versions of upgraded designs should not appear anywhere after they are discarded from the shipyard screen.
Also, slightly off topic, but it would be absolutely wonderful if somewhere in the reports Galciv2 would display a fleet summary screen, telling you how many of each ship class you have in service (rather than just a list of each individual ship, which becomes unusable the further into the game you get).
This is a pretty good game and certainly its the best turn based strategy game on the market, but the ship design feature, for me at least, is a major turn-off. The strange problems with it only make it worse.