Some ideas I've heard from people over the years...
1) Be able to make a ship jump out of the area and then jump back in at a later time.
2) Be able to "transition" from mission to mission. In other words, be able to go from one mission into the other without having to show an "Incoming Message" screen. With this you could create a series of missions that would simulate moving from one system through a jump node to another before returning to base.
3) Be able to have more than four ships in a wing without problems.
4) Be able to use other wing names besides Alpha, Beta, Gamma, etc. and still have the benefits of the wing/ship status indicators, etc.
Reality check : As a software engineer myself, I think first someone should look at possibly writing code that would implement precompiled in-process files (e.g. DLL). That way we won't have to package and compile the code all over again when someone creates a new addon, for the most part. This would definitely be helpful in FRED to be able to create addon DLL's that could be implemented into the FRED environment rather than ending up with dozens of tools that everyone uses all running in separate processes.
Rock on!