Some ideas, apologies if these have already been suggested.
1) Some way to move missiles as cargo. Magazines can hold up to 20 MSP per HS, so allowing missiles to be 'crated' into cargo holds at 1 MSP per HS (or 100 MSP for a standard Cargo Hold) would not be unreasonable, and provide a way to ship them between bases. They would have to be unloaded at a planet before being loaded into a magazine, so you could not transfer missiles from a cargo ship to a collier, etc while in space.
2) The ability to contract minerals and population (and fuel? civilian tanker designs?) for transport by civilians.
3) Ability to order speed changes through the orders list, the same way one can activate sensors and shields.
4) A way to activate active sensors independently for each ship, rather than all on or all off.
5) Some more incentive to build orbital bases. Currently there is very little reason to do so, as PDCs can easily be much bigger, and orbital bases require a shipyard. Either allow them to be built on planets as orbital habitats are, or maybe allow shipyards to build orbital bases up to 2x or even 5x their maximum 'ship' size.