First up, yay for ship transfer, but not instantly. Modules, maybe - but if you've got ship transfer, you may as well have modules too...
I've tried to read through the reams of comments on here - and seen a couple close to what I think would be a possible idea. If it's a repeat then sorry.
You should be able to request your ship to be transferred from anywhere to anywhere whilst you are docked. This anywhere to anywhere should still be limited by the ships capabilities. If you can see your ships setup from any station, perhaps you can remotely organise for a fit out with a bigger FSD if that's what you need. You shouldn't be able to get ships to places they couldn't otherwise be.
Generate a "Ship Transfer" style mission made available at the star ports where peoples ships are held. Perhaps based on ranking to ships worth, allow useless pilots like me nothing more than accepting a mission to deliver a sidewinder; whilst those elite types would be allowed to deliver the biggest kick ass monsters. Recompense would also be in ratio to ships worth and distance required to travel. I'm sure for expensive ships over long distances, this would be very large. Players can also offer a bonus for quick delivery - just like in the standard missions.
The ships route is locked to non-anarchy systems, policed only, to try and prevent theft (I guess like a permit system, but only for that particular ship/route). Unreasonable deviation too far from the route or tardiness during delivery (unless docked in a space port) results in heavy bounties, and increasingly large amounts of hassle from NPC police types, or even other players - again to dissuade from theft.
This being the case, the ship being transported should then take a realistic amount of time. You may get to fly something you haven't before as a result of the mission. You still get the same risks as normal with moving your ship around - being attacked, flying in to space stations, dropping in to suns etc. (yes, I know those of you more experienced ones don't do this anymore - but that's why you're allowed to fly the big ships).
The insurance cost for the ship being delivered must be available from the mission takers bank balance - so if they trash the ship, it costs em. It should be taken at the start of the mission, and held as a bond until delivery. For the mission giver, this means that your ship gets at least replaced without cost, your replacement ship gets ordered at the last station docked in (as per normal play I think) and whatever part of the route has been covered up to then isn't lost.
As no one wants to wait forever for someone to take their ship delivery mission, if the mission isn't taken within a specified amount of time - then an NPC takes it (maybe as an addition, the mission becomes available at each station the NPC must dock at for fuel or whatever, for a player to take over if they are there during the docking time). If there is a fuel scoop fitted, then the amount of docking opportunities would of course be reduced. If a player only wants to carry out part of the mission, then they can leave the ship at a space station on route - and get paid for the part of the journey they have done, less an administration charge perhaps ;-)
Of course, once ordered - you go off and do your normal thing. You can see where your ship is currently, be kept updated regularly. With forward planning, if you know you want your kick ass ship at x, then order it before you start to travel there. If you're already there, just pretend its like waiting for that Sunday delivery of an amazon parcel... It always gets there in the end, even if that's sometimes Tuesday whilst you're at work ;-)
Modules could be dealt with in a similar fashion? Cargo taken, but insured in advance by the mission taker?
Last but not least, if you take a delivery mission like this, then when you get to your destination you are minus a ship - unless you of course already have one of your own there waiting. Perhaps you can get returned as a passenger mission, or are given something small like a sidewinder to make your way back in. That is unless of course with all of your newly earned credits you buy yourself something shiny and fun...
I'm sure that the above is full of holes - but then again, I'm sure some of you can help fill them

ducks and runs for cover
Cheers,
CMDR UnahaClosp