Since this thread has been resurrected from the depths of the thread grave anyway, I figured I might as well post my own idea on this matter.
The best way to implement multiplayer in Orbiter would IMHO be similar to [ame="http://www.orbithangar.com/searchid.php?ID=4331"]Real Time Update[/ame]. If you don't know what that is, or fail to see how it would be relevant to multiplayer, I'll explain exactly what I have in mind. Each player controls one ship of their choice. In this scenario, there are a number of ships in the simulation, each controlled by a different player. Time warp is disabled. Just like in a normal Orbiter session, each ship moves along its trajectory, according to the laws of physics. However, unlike a normal Orbiter session, the ships would continue to move along their paths even when their pilot is disconnected from the server. When the pilot reconnects, they pick up the ship from where it is at that moment. Let me give an example: suppose you want to fly to the Moon. You fly to orbit and perform the TLI in real time. You can now disconnect, while the server continues to simulate your ship. Three days and maybe a couple of MCCs later, you do the LOI and land at Brighton Beach just in time to meet up with your friends, who also did an Earth-Moon flight.
No, this system is not perfect. I don't claim it to be. However, I think it could work in practice. An important disadvantage would be the fact that you are pretty much "banned" from the server for the duration of your trip. This could be mitigated by giving each player more than one vessel, or allowing them to spawn new vessels at a predetermined, fixed location (up to a reasonable limit, of course. We don't want the server to crash because someone decided it would be funny to spawn five hundred XR2s.) Another problem is that a player might not be able to connect at a specific time for a maneuver, but this can be, for the most part, avoided by careful planning of the trajectory. Besides, most maneuvers one would perform under these circumstances aren't very time-critical (if one is willing to wait up to a few orbits), an important exception being the LOI.
Mars, Venus, and Mercury would be reachable with enough patience, but anything beyond Mars is probably out of the question.
Certainly, there are a lot of disadvantages to this system. But it's the best way I see, and I think it could work (perhaps with a few modifications).