Personally i would like to see more costly upgrades for everything. For example i would like to see 13k shields for fighters that cost 25k, then 15k shields that cost 50k and so forth upwards of 250k. Those upgrades are not suppose to be common, they are suppose to be unique that only few have just like the cap armor 8. I simply would like to see more opportunities, not just stop once you max out your fighter with only few mill. This will hopefully make people think twice before cheating also.
I would also like to see difference in speeds between classes. A light fighter should not have the same regular speed as a train.
Upscale the size of the systems (such as O81) so the battleship is not the size of a planet. Probably would require tons of modding so its not that important.
At last and most importantly: GET RID OF THE DARN MOD MANAGER. Make installation of the patch as simple as downloading DiscoveryMod486.zip, extract the zip out to a DiscoveryMod486.exe, double click the DiscoveryMod486.exe file, click Yes i would like to patch Freelancer to Discovery mod 4.86. and watch it extract your files. This is not only to make installation simpler however to eliminate the chance of accidental cheating for newbies. This way people will have to go out of their way to cheat as all the goodies such as the speed mod is not available to them right on their screen.