The biggest problem is the companies that take their classic, venerable JRPG franchises and attempt to turn them into something they're not. Recent releases under the Final Fantasy banner are a good example of this. If more games were released that were proudly old-fashioned (Ni No Kuni, Fire Emblem, Lost Odyssey, Etrian Odyssey, etc) the genre would be in much better shape.
In many ways, Square is sort of trashing the image of JRPG and mucking it up with wild, sometimes ill-befitting gameplay ideas that make it appear as though the genre is in decline.
There are just two different paths developers are taking JRPGs in. One path is to try and alter the fundamentals to appeal to a western audience (sometimes with mixed results, sometimes successful), and the other path is just to carry on as if nothing has changed and sell to your loyal fanbase, sometimes attracting new players.