FS1 port is good, as is Silent Threat Reborn, and those can probably be done while you are still getting your skill back. Blue Planet is excellent but can be difficult. Ancient Shivan War is my favorite, and is not very difficult.
Windmills is good and unique, different from what you may have played before.
There are at least three major releases, non-universe mods, as well: Wing Commander Saga, Diaspora (Battlestar Galactica), and Wings of Dawn.