I have recently played a bit with FRED (3.6.13), and I decided to share some suggestions here.
1. This may even be a bug. The wireframe mode (only show outlines) is very slow, to the point of being almost unusable even on my new machine, and with only a few ships present. It is weird because when I enable "show ship models", it works flawlessly.
This brings me to the reason why I decided to disable show ship models - when i try to select ship with models enabled by pointing where the model is, I actually find out the ship is not there, but a bit off (when I disable "show ship models" the wireframe model shows the ships true position). In short, the model is not rendered in the ships real position, but with some offset. This is PitA especially when selecting smaller ships or fighters from a greater distance.
2. The wireframe model is always dark grey, regardless of the IFF. The old way (friendly blue or green, enemy red etc..) was much better IMHO. Dark grey always blends into the background, which is usually dark too.
The wires should also show up superimposed on the model when "show ship models" and "show outlines" is selected at the same time. Just like old times.

3. Mission designers would certainly appreciate if weapon editor could be used to edit turrets on multiple ships at once (assuming they are the same class), just like fighter weapons can be now. Setting up for example sentry gun fields would be far more convenient this way.
Just my 2 cents

Anyway, keep up the good work!
