This has been requested in quite a few threads lately, here's one
http://forums.startrekonline.com/sho...d.php?t=195027 and it has links to a couple of others.
With the new Duty Officer system and Shuttles coming out I hope this is addressed, because it is sounding like this is a major issue for a lot of players who might not try out the new systems otherwise. Yes, it's nice to be able to get into a shuttle and do a special mission, but if every time you do you have to completely rebuild your user interface that's a bit of a problem.
Personally, I think the current system just needs to be tweaked, it seems to save slot information, but then loses it if you don't follow the rules very precisely. For instance, you can't assign two abilities you wish to switch between to the same slot, they have to be two different slots. So in effect you need to leave empty slots in both your builds. This is clearly a hassle once you start to get short on tray space.
If you could save and load a tray arrangement that would be nice, but it would involve the extra step of having to save and load the tray, every time you changed your ship or loadout. If the trays just didn't get messed up in the first place it would be better. As a quick fix, though, until such time as the bugs in the implementation can be tracked down, it's a good idea.
I posted an idea in the thread I linked to, basically you could use the Powers Window to assign slots to your powers and that would "lock" them into that slot if available.