I don't think gameplay is the problem at all. I think the genre becoming more niche has to do with the stagnation of the story archetypes that have dominated. It's getting to the point where the characterizations, character dialogue, motives of the antagonist(s) and the general themes, are all being repeated, and at a grander (and more intrusive) scale due to the growing scope of these projects.
How many JRPG's over the last 5 years have portrayed teens fighting againt a powerful group or entity that wishes to eradicate humankind in an attempt to cleanse them of their sins and start the world anew? What about the characters? I bet one of them is a hot-headed boy that that has trouble coming to terms with the grey area of morality. Here are some more: the mysterious adult woman, the musclehead who likes to eat, the secret princess who wants people to like her for who she is, etc. I'm not trying to say that any JRPG that contains these should be considered bad...a game like Ys 7 contains a lot of these cliches, but they are in the background, not the foreground, while games like FFXIII or SO4 are thrusting them down our throats at every oppertunity.
I think what we're seeing is that these "mainstream" JRPG's are dying. Sands of Destruction, White Knight Chronicles, Final Fantasy XIII, Star Ocean 4, etc, all arguably had that rinse-repeat feeling, while JRPG's that either attempt to deviate from the these cliches, like Persona 4 or Demons Souls, or take a simpler, classic approach with the narrative and characters, like Dragon Quest and Ys, are those that are being embraced.







