I'm not a big RPG player, but I feel as though many of the games labeled as "RPGs," including the majority of the JRPG sub-genre, don't really fit.  For me, the key lies in those first two letters; role-playing.  When I think of the original D&D archetype all of these games are based on, it's not just about rolling a D20 in an encounter or leveling skills on your character sheet, it's about actually fleshing out a character and putting something of yourself into them.  Look at the great BioWare titles like Star Wars: KOTOR and Mass Effect, where you decide most of how your character interacts with the world around them, even down to their gender and relationship preferences; that's pretty much the definition of taking a role and making it your own.  Then compare it to something like Chrono Trigger: even though it's a beloved classic that I enjoy very much myself, there's little to nothing I can do to affect how Crono behaves as a character, and the overall story is extremely linear.  Those are two extremely different philosophies of game design, and I think that labeling them both as "role-playing" is something of a disservice. 
So then what should we call games like the mainline Final Fantasies as an alternate?  Hmm..."stat-based battling adventure games"?  Okay no that's pretty terrible, but you get the idea.