The only semi-major issue with fred2_open (3.55) I can think of at the moment is that it cannot properly load missions with the
support ship hull repair cap enabled, much less edit them. The game can read these missions fine, but the editor gives an "Unable to read mission file" error followed by an illegal operation message.
Additionally, there is a bit of an annoyance with the Windows associations for the .fs2 mission files. I usually like to have these associated with Wordpad or some text editor but if I change the association, fred2 always steals it back upon opening the program, even though it cannot load the file like that and just starts up normally.

The best thing would be to just delete this association-changing code altogether.
It would also be nice if some of those BS error checker messages were removed (no players in alpha wing, starting wings' orders do not match, etc.).
One other thing I have wanted to see for a long time is the ability to customize the keyboard controls used for camera movements. I have no idea how difficult this would be to do, but it would be great if the editor uses the controls from a specified player file instead of just using the default settings. I have changed around some of the controls in the game, so it is slightly inconvenient to have to use the default controls in the editor after getting used to a different setting in the game.