I've been playing Freelancer since the very first day it hit the shelves in the US and enjoy it a great deal. I look at this forum several times a day though I've never posted simply because there are a lot of good ideas being posted already. I cannot resist anymore though, and probably my greatest desire for this game won't come true until a Freelancer 2, if we are lucky.
I wish I could make a "real" difference in the Freelancer universe. Sure, more mission types, more ships, more weapons, blah blah blah would be great, but personally I would give up all those things for this version of the game if the things my character did made a difference of some kind. For instance, some Kusari police were mentioning how they wish they knew where a jumphole was so they could patrol it for Outcasts. If it were my inclination to help them, I would love to be able to find this jumphole and sell them this information. And an effect during gameplay would be that Kusari police now have a patrol near that jumphole for the rest of your game.
Eventually reducing or virtually eliminating the presence of certain pirate or corporate activity through destroying many of their members, if even for only a certain number of game hours until they recruit more, as someone posted recently.
Where are the bounties for attacking criminals? During the rumor process, I hear about bounty hunters searching for specific criminals. I would love to be able to cruise around that system or go to another one, searching for this person too, and actually find them before the other bounty hunters do. By the way, I love the exploration aspect of this game and so this idea greatly appeals to me.
Another idea on making a difference, I hear "rumors" that the station or planet I am at would love things such as mining machinery and would I please go get some... I'd like to feel like it meant something if I did, maybe receive a thank you from these people. The "best" trading routes would become less important if my helping to deliver goods to, and protect ships of, certain groups would help make them more commonly seen in the universe, proof that I wrote my name on that wall.
I guess what it all boils down to is that I feel a certain roleplaying aspect missing, playing as a single player, which I had hoped would exist based on what I had read about Freelancer before I got my hands on it.
I just hope that some DA deity thinks it important too.

one thing that i think should really change is the option to drag-n-drop waypoints from the AI's Best Path function.

that way, when you wished to only change a point or two in-system <like going to Base X instead of Base Y because you know X has that nice shield you just got the cash for> you could keep the overall insystem path and just pull one or two points around for a different path. That would also take care of jump holes.

that would only work for insystem paths, of course, but many times i have wished for this simple function.