In a realistic universe (and I am speaking of even "realistic" Sci-Fi, like Babylon 5, Star Trek and Star Wars), ship design is:

1- Costly
2- Lenghtly

I find it quite.. streched to have automatic and free ship designs, ones that works on the first try, with no prototype to build, and no tests to run.

I think the game would be less imbalanced in our favor (intelligent players) if there was a time and money cost to developping new classes of ships. Or implimenting new technologies for the first time on a ship.

It would be nice if we either had to "research" the classes of ships we choosed the specification, or at least wait a few turns before building it.

And if we want to add even a little more flavor to this thing, we could put a random money + and - to build, or changing some technical specifications. After all, not every ship designs who looked good on paper ends up effective. If you have a good streak of luck with one peticular design, it would really influence your shipbuilding's choices.

(example: Mister President! Our engineers cleverly found a way to reroute the engines power output to the shield systems, making the frigate 7% less costly to built)

(another example: Emperor! The scientists screwed up, and our new fighters has a major flaw in it's design, making the Phaser cannon 20% less effective.. I'm sorry.. arg.. can't.. breath... ...)