Well, usually because the gameplay is awful. Don't get me wrong, I love FFIX and FFX and many other JRPGs like Chrono Trigger or Persona 4. But I can't deny that the actual fights in these games are lame, boring and EXTREMELY repetitive. Casting Bufu once on a monster to knock it down is okay. Casting Bufu 500 times on the same monsters is more than a LITTLE ANNOYING. Granted, some fights in JRPGs require strategy, but those are rare and usually don't come up in the main story line of the game.
What saves JRPGs are the story and the artwork and the music. FFIX had a great story and even better music. I loved to play that game for the story. With JRPGs, you can measure how good they are if you can BEAR the random encounters and battles for the story. This is the reason why I couldn't stand FFXIII - the story, to me, was bad, and the characters downright annoying (except for Sazh). And if a JRPG has a bad story, there is literally NOTHING good about it, so when a JRPG fails in the story department, as they have been doing recently, they fail colossally.
I mean think about it - there's really no RPG element in a JRPG, since you don't play a role. You don't really have that much control over your character in battle, and the battles themselves get very repetitive, very quickly. So what is there to a JRPG, EXCEPT story, music and artwork?
And some people don't like the story, or the art work. So for them, a JRPG offers nothing. I mean, absolutely nothing - if you don't like the stories in JRPGs, there's nothing for you - they are supported solely by their characters and some people just don't gel with the typical cast and characters found in JRPGs. I, myself, am becoming increasingly exasperated with the "brooding pretty boy" stereotype found in a lot of JRPGs - probably the reason why I liked FFIX and FFX so much, because in those games the main protagonists were cheerful and optimistic, instead of whiny and sour.
For JRPGs to make a comeback, the designers have to start taking risks. Don't follow the standard anime tropes and cliches. Please don't follow pedestrian story structures and overused themes of "friendship" and "love".
My main point is that what makes a JRPG great is not the graphics or the gameplay. Persona 4 was a great game, despite being on the PS2 and having atrocious gameplay, because it had a pretty good story and a cast of likeable characters and great, stellar art-direction. FFXIII was, in contrast, a bad game, because the story was extremely limited (Almost no NPCs, towns or characterization of the world), and I found the characters, especially Hope, to be incredibly dim-witted and whiny.