I've recently had a few simple feature ideas:
1. Gun recoil:
This might have already been proposed somewhere, basically a table setting which would let a weapon to substract a value from firing ship's velocity every time it's fired. It would be mainly usefull for high power ballistic weapons.
2. Piercing on "overkill":
An addition to normal piercing effects which would allow piercing to occur when a single weapon hit is going to take the target down, regardless of it's HP left. So, if you have a cannon which will take fighter from 100% to 0 in one shot, then it'd have a piercing effect, despite hitting a fighter which is at 100%, not at 10.
3. Shot casings counter:
Currently, if you have a ballistic shotgun primary, ammo counter will display number of pellets left, which is irrational. A launcher flag could be used to make counter display number of shots left, which would be more intuitive.
4. Hiding FS2 main campaign:
From time to time, somebody makes a mod which is still dependant on FS, but so different that FS2 main campaign will not work with it. Unfortunately, there's nothing preventing people from running the main campaign (it's selected by default) and reporting the problems as "bugs" later. So, I think that mods could use a way to hide FS2 main campaign without causing crashes. There's a hack that allows doing that, but it can cause problems when switching mods.