I group fanfics the same way I group icons: FFX/X-2 are the same fandom, FFXII/RW are the same fandom, FFVII and all its Complicated children are the same fandom. The continuation of plot threads and characterizations seems to be the deciding factor for me, rather than simply character appearances or settings. I consider Dissidia separate from all the above, despite having the focal pro- and antagonists of the main series games; it comprises its own fandom based on the differences in gameplay, plot, and development of the characters.

I grouped the non-XII Ivalice games together because I've never played them and don't know much about them, but after reading lassarina's comment, I suppose they should be separated if I were to use my plot/characterization criteria.