One thing I really wish we had

[Batman]

In some respects the idea of qualitatively different costs for construction and maintenance doesn't make much sense. S-J, to use your example, surely the intial cost for a psychic weapon like that would need to include some organics to represent the cost of (breeding/training/growing) the psychics, and a smaller amount to maintain the group (provide replacements etc). The cost of building a component has to take into account all of the individual costs, no matter where they come from (presumably the cost of crew quarters takes crew training into account etc)

However, I would like to see maintenance tied into the age of the component (probably impossible with the current game code). Older components should cost more to maintain, with the clock being reset every time the ship is retrofitted.

[Suicide Junkie]

If your population has natural talents, you don't need to do much training.

PvK's examples are better; use the armor (no maintenance) vs engines (fuel maintenance) idea.