I would really like to see ship upgrades limited to units in "drydock". That could be at its simplest, starbases and shipyards. Or, better, at a shipyard, and only at a starbase with ship maintenance facilities.
On that note, though combat isn't out yet, I think crews should only be able to restore a limited amount of a ships combat damage on deployment. Repairs beyond this, should only be accomplished at yard facilities/designated repair facilities.
This would allow for a much more immersive and realistic game universe.