Wing Commander Prophecy.
1 Fighter per squadron.
Keep the interactive conversation thing.
Fix the full guns slow rate of fire issue.
Give figures from the old games cameo roles rather than shoehorning them in for no obvious reason.
E.g. One mission or campaign involves helping the Border Worlds, cue cameos from Hawk, Wilford or Decker.
Maybe have the Midway relieve a Confed station under Blair's command (cue headline, Old Warhorse saved by his own
White Elephant).
Keep cloaking and autotracking guns (maybe fewer missile or ship types if you have to).
Close up the plotholes (how did they manage to acquire the Alien Supergun anyway?)
Secret Ops
Proper cutscenes (maybe as old Wing Commander style talking heads).
Note: Neither of the above games were terrible, nor were they spectacular, and a few changes could have breathed new life into
the franchise, if not the Genre. However, this leads to the final nail in the coffin for one of the greatest franchises of all time (Freddie Prinze Jr. being the first).
Wing Commander Arena.
Keep to the old Wing Commander format i.e. 3D flight sim. 3rd person perspective by default to keep the console punters happy if you must but first person would still be cool.
A PC version.
A single player campaign. Maybe winning certain medals or achieving certain ranks gives you different bonuses in the Multiplayer mode.
Less reliance on previous designs. maybe have the basic of each type as Arrow, Rapier, Broadsword have different designs rather than variants. Or perhaps have an original fighter design as unlockable.
Border Worlds as third playable faction rather than having them screwed over in the manual's fluff.
No reference to the movie at all.
Privateer 2.
Actually make it resemble the universe in which its set.
Keep the original character from the first game.
Maybe present it as the civilian side of the post Kilrathi war galaxy.