I think FFIX gets underrated because it doesn't really tap into a primal themes like other FF's do. Zidane goes on a journey, but it is not the same as Cecil or Cloud, so when you break away from that traditional mold, you are going to lose something with the masses. It is also going to lose something in translation generally, because those primal themes are so strong, and FFIX is all about tweaking archetypes, so everything seems kind of strange because so much of how the characters develop is not what you would expect.

For me, that is the main reason why FFIX doesn't get the same kind of love as FFVII, IV, or X.