As for controllable ships, simply download Freelancer Mod Manager 0.7, which comes with a couple mods, then download the Ghost Docking Rings mod in the same topic on this forum.

Wanderer has like a hundred different tutorials on this forum to make ships pilotable, just download an ini extractor from this site and follow the instructions. Simple.

People are working on encounters of big gun ships, but I'm not aware of any working examples. Pretty much everything here is a minor game tweak, so you'll have to wait for actual mods to come out and work.

"I think this hold full of toxic waste will secure us a good price."

Actually, there already are mods that put battleships as encounters, or so they say. I'm trying to reverse engineer one myself to incorporate my own brew of custom battleships.