Originally, it was because people only played up from FFVII and/or FFVIII, and didn't get it.

Now that people have had opportunities to play the Nintendo and Super Nintendo eras. People want to hold on to things like the "downgraded" graphics and character models and try to say the game is all "Kill Kuja" and of course get angry when FFIX fans argue that FFVII is just "Kill Sephiroth." Because they know deep down we fans of the nostalgic enigma are correct in saying that FFIX is just as good as any other Final Fantasy made even rivaling FFVII. I know I may get countered with Cloud can Omnislash away Zidane's Trance but the fact that Zidane doesn't an attack that does 15 hits of 9999 damage nor does Garnet/Dagger or Eiko have have a summon that does 13 hits of 9999 damage means you actually have to strategize to win battles, and people don't want to have a challenge which is something you had to do back in the days of NES.