I would simply like it if we could give our crew something to do. I'm not talking about X levels of precision here where you can see the exact move of every one of your ships. I'm talking about something more simple, like Euro Truck Simulator wher you hire a driver give him a truck, tell him (or her) what to focus on and away he goes. You won't see the crew member in the game (even if you happen to be in the same system as him) but more simply just his status i.e "flying to lave to pick up missions", "transporting slaves from station x to station y" eta 20 mins etc. you see say 20%- 50% of the profit he makes & have to do (or send him to do) periodic maintenence on the vessel as it starts wearing down. You could also use him to transport your ship from A to B providing it has the range for it, if it doesn't he should be smart enough to go to the nearest base that has the required modules, store the ones that are on the ship and kit it out so it can make the distance before taking the trip (modules stored will travel separately).
As for the cost of transporting vessels I would break it down into a high rate one for ships that are not currenly crewed (complete with modules & all) or a low cost model if your ship is crewed, maybe even just the standard rate of pay for the crew member. Transporting a ship via the current method should stay the same as it is i.e. the ship is complete with it's required modules in the same condition as it was when it started the journey. A ship transferred by crew member, will have sustained some wear & tear (depending on the distance jumped & will have to be refitted to it's new role once it gets to it's destination using your stored modules.