I think a system could be developed where both the real time travel and the rapid transit travel could be used within the same game.
For example:
- If you are out and about just meandering through the universe exploring, why not use a realistic travel model that allows you time to access on baord systems, run some sensor scans, participate in some holodeck fun with friends and further train your Starfleet officer. This would be an excellent model and would make Ship Interiors much more justified. Furthermore, if you were about to log off for the night, your guild (ship crew) could set a course, and you go off duty to your quarters and simply log out, then when you log back in, you are in the destination system and can begin some missions and stuff.
- Rapid Transit could be used when accompanied with a mission or if you are covering ungodly amounts of space between set points (much like Flight Paths in WoW). This would make multi-planet / multi-system missions much easier to take on. However, you could also be allowed to take a slow path during missions if you chose, where that time could be used to conduct work for the mission on ship such as scientific studies, long range scans, research on an enemy, tactical / security training, etc.