Sorry to rez a (slightly) old thread. But it seems to me the whole time acceleration problem could be solved by a firefly style vessel.
Obviously the Earth-Moon system wouldn't have them, but for interplanetary routes a large firefly style carrier vehicle controlled by a high level player/admin/pretty good autopilot would be utilised.
Players buy docking space on the carrier vehicle, which is scheduled to depart at time x to destination y and costs z currency. Using a highly modified FF drive, the ship could get to mars in 3 days and other destinations in a similar amount of time (These vehicles would have to be absolutley massive in order to house the engines, the inertial damper device, the fuel, and the 30 odd vessels attached to it). As it is just the FF drive, real physics are implemented all the way their and back, and time acc problems could be avoided.
That said, these vessels could be a major part of the MMO economy - having such a large and dedicated vessel would require significant amounts of consumables to operate - players could receive a discount for using their own O2 from their vessels en route, and other players could mine materials to refuel and repair the vessels at either ends of their routes.
In addition, a World of 2001 style system could be implemented - any non-critical cargo could be flung from earth to mars under ai/player control and so on; REALLY dedicated players could fly from mars/earth with less powerful FF boosters, or even no booster at all. Obviously a player who makes an Earth->Mars trip in real time would have to receive significant rewards and brownie points.
This all said and done, having UMMUs able to interact with vessel interiors, structures on planets, etc. would also be a major leg-up. Also, perhaps the economy could be based on the Hydrogen Peroxide economy of the '__ Mars' novels, every item/vessel has a value measured in minerals and consumables.
Finally, i would absolutely LOVE this MMO - Orbiter with other players? In a custom Univers? HELL YEAH!
(PS: Space elevators could also be implemented on either end - but large waiting lists due to traffic encourage you to fly in manually)
EDIT: As an initial proof of concept, if we can get a large orbiter simulation of the Earth-Moon system up and running, we could always add other areas in later. An MFD could warn you if you're about to go 'out-of-bounds' and warp you to the closest allowed orbit if you enter the no-fly zone
Also, where can i get the mission control add-on and OMP, i'd like to have a look at them.