X3 is indeed a newer version of X2, with updated graphics, balancing (no one ship to rule them all), updated economy and bigger.
X3 2.0 : Bala Gi research missions has most of the bugs patched (DO NOT play X3 1.0 without patching first), there is several player made scrips added that enhance the game, as well as the Bala Gi part which adds new items to the game such as the MASSIVE player owned Head Quarters station.
Freelancer i would consider a arcade spaceshooter version of X3 (ignore that freelancer came first). When fighting Freelancer plays very similarly, and has a limited trading system (you can buy and sell items for profitssss, but it'll take a few years to save up for that new ship). X3 is more lacking in fighter combat but makes up for it in fleets and massive economy. But be warned that you'll sink more hours into this game then a RPG if you intend to play it to it's fullest.
The story line is secondary to the sandbox part of the game, but i recommend doing the first 2 or 3 missions to make things easier when starting out.
Also note that there is a very large and active modding/scripting community for X3/X2. If you find something in the game you don't like, chances are that so did someone else who made a script/mod to fix it. There is a player made script installer that makes the process VERY easy.
Then there are the mods, the most popular be the XTM mod that makes the game more alive, aggressive towards you, MUCH bigger, new (and nasty) ships, improved AI BUT at the expense of stability, possible broken plot/story, and it'll become a system recourse hog.
If you have any questions, search the X3 forums, then ask in the right forum and you should get all the help you need (unless the community has drasticly died off since i last played). Oh and f*s, don't ask when X4/X Online is coming out, it's asked once or twice EVERY week and long time members get real sick of seeing the same thing over and over again.