GalCiv2's design-it-yourself units had lots of visual customization, but the barely-a-combat-system rendered the actual ship design simple and pointless.
In the Master of Orion games, I rather enjoyed designing ships that work together in special ways, or that use abilities that the AI usually neglects. In MoO2, I once made a race of pirates that used tractor beams to halt enemy ships, punch through their shields and then boarded and captured them. Then I reverse engineer these ships to get the 'usual' techs while I focus my research on the unusual things.
Although MoO2 had more cool abilities that one could use, in MoO1 the AI was capable of using more of them effectively. I think the simpler battle map and tighter combat mechanics made that possible.
The reason why I'm considering pre-designed units at all, is that it can really bring out the character of the species. (e.g. StarCraft, or the Battle for Wesnoth)
Then again, I have fantasized about a game where you could design your own weapons/systems and put them in ships that you also designed. Now that I've actually played something like that (Aurora, I think) I know that it could lead to tons of boredom. (Yes, boredom is measured in tons.
)
Over the years I have come up with two ideas on how my game's combat system could work.
The one is similar to MoO2 (small 2D tiles with large ships), except with cover, line-of-fire and friendly fire added, so that placement actually matters.
The other is a 1D series of battles at different orbits and being affected by different defense systems. (Like in Anacreon: Reconstruction 4021) But more varied by using special commands. (Like in battles from Final Fantasy V or VI)
And recently I've been thinking of the potential of Master of Magic style battles, with spells replaced by various long-distance abilities.
Anyway:
If I have fully designable spaceships, I will keep the number of item slots very low to encourage having specialized roles.
tl;dr:
Now that I'm discussing this with people, I'm suddenly having new ideas. And writing walls of text.