I'm probably going to make everyone in these forums hate me for saying this, but in a way, I'm glad that FS3 never came out.
I really like the fanon that has developed over the years, the Derelict, Casualties of War, (and eventually BWO) type fanon is nice because it adds on to the original story very well. Sync and Transcend both literally scared me. Homesick, I dare say it, made me want to cry. The original Freespace campaigns never stirred up those kinds of feeling in me. If the FS story didn't have so many loose ends, people wouldn't feel obligated to tie them up.