Chris Knudsen is planning to add a storyline to Privateer: Ascii Sector. The project has a forum where you can comment on this and other plans for future development. You can also submit bug reports there.
I've managed to maintain save game compatibility since the first release two years ago, so that shouldn't become a problem. As to adding a storyline; yes, that's definitely something I have planned. It will kinda be split into two parts. The first part will have you flying around in your own ship, doing various missions and getting involved in some shady business. This will result in an event that will cut off the sector from the rest of the universe and cast it into a massive war between the various factions. At this point, you'll be able to buy your own base (if you have enough credits) and start building your own fleet to attempt to take over the entire sector and restore peace. There will be some strategy and RTS elements, as you control your fleet(s) in battle on board your flagship. You can read more about my future plans in the "Development Discussion and Suggestions" forum of my board.