I'd love to see a subgame of a Star Trek MMORPG where players could, within limits, create their own starships. In fact, I'd say that a big part of the fun in a ship design feature would be working within appropriate limits.
Restrictions on options -- not arbitrary "just because" limits, but reasonable requirements and tradeoffs -- are what enable interesting choices. Otherwise everybody would just build the Biggest whatever, and how much fun would that be?
If the available warp cores were rated for size, mass, and power output, and then every possible powered system were rated for size, mass, and power usage, then for a given hull type the Naval Architect game would be to optimize components for a desired mission profile.
For example, suppose you wanted to build an assault shuttle. You'd start by selecting the appropriate shuttle hull. Then you'd start choosing systems -- maybe you start by picking your powerplant, then weapons, or maybe you choose subsystems, then weapons, then try to find a warp core that will fit into your hull while providing enough power for your chosen systems.
Sound like fun to anyone else?
If something like this were ever implemented, it would need to be folded into the rest of the gameplay. For example: let anyone build a starship, but hold design competitions to see which ships are selected to enter service. Maybe all the player Admirals can get together once every three months (or so) to decide which of the currently submitted designs best meets the projected needs of Starfleet. Maybe the Federation needs some help in the diplomacy area, and the best fast courier design would win.
Obviously I'm just scratching the surface of the possibilities here. The main thing is just to note that it would not be correct to consign a naval architecture feature to the "simulation" circular file -- it could, if smartly implemented, make a positive contribution to gameplay.
I like to think it would even bring in enough paying subscribers to be worth the development time, but that might be a little too enthusiastic of me. :)