Finally, I think I disagree with what you said when justifying why you are using the RPG genre, "The JRPG side of course lends itself well to storytelling, which is a prominent focus of the game." This statement is not completely true, because the RPG genre doesn't have anything that gives it any type of advantage over other genres in storytelling. The genre used to have that advantage because technology didn't really allow other games to include anything extraneous to core gameplay. The real relationship between an RPG's mechanics and story is that the game strives to tell a long story and the best it can hope for is that the gameplay doesn't detract from the experience, let alone add something. The Extra Credits episodes have maintained that RPGs cater to the aesthetic of Abnegation; they succeed when they are giving you something very simple to work toward in order to keep you invested in the story it is trying to tell. I just think that you should keep this in mind before saying that you want to use RPG elements just because you want a story focused game.
That's fair, and it's important to determine why we play J (3rd person) RPG's and what makes them good for storytelling. I've actually determined that my core aesthetics should be Narrative, Abnegation, and to an extent Challenge (so pretty much in that order). Gameplay wise, I might disagree that turn-based RPG gameplay "doesn't add something" to the experience, depending on what you mean. I actually like turn-based battles, simple as they generally are. (I'm also using some tactical mechanics in the battle sequences as well, kind of like a small-scale Fire Emblem, so they stay interesting). I also want my game to be a game, not an interactive novel, and I don't really want to emphasize puzzles (at least not what you normally think of as a puzzle), because puzzle-solving is more out-of-place for my subject matter than combat. And most importantly, keeping Narrative the focus, I plan on using combat for unique character development opportunities.
As a rule of thumb, I don't play multiplayer games with have persistent leveling systems. I can't even imagine one being done "right". In single player they can be used to set the progression of the game so that you unlock stuff and in the end of the game you have everything unlocked, beat it and forget about it. This is classic single player system. But in multiplayer this means that players who play more get more options to choose from which in the end means they have unfair advantage. And if the only way to get on par with other players is so invest more time or real money, this means that the game exists for the sole purpose of sucking money out of the player, not providing good gameplay experience.
I'd like to point out the Assassin's Creed multiplayer here. The gadgets are a plus, yes, but they're ultimately the second best weapon you have other than your own ninja skills. (But then there are the clown running around like it's Battlefield of Halo, somehow getting first place with a boatload of points.
An RTS that combines RPG elements like a branching storyline, whereas instead of the isometric view from the above, it takes a 3rd person view behind the player avatar. This game is about battling wizards, each players gathers souls to summon creatures, and then duke it out with other wizards, also supplemented with various spells. Their goal, based on the name, is to find an enemy altar, desecrate it by performing a sacrificial ritual on that altar, and then kill the enemy wizard one last time to banish him. = Sacrifice from Shiny Entertaiment. Released in 2000, the same year as Deus Ex.
'Combining Genres' said NOTHING about why it makes sense for Call of Duty to have a reset button, when traditional RPG's wouldn't think of it (except maybe Breath of Fire IV, and Dungeons and Dragons Online in the MMO world). They only hinted that there were reasons that it made sense for Call of Duty.
RPG's don't need a reset button because the new game feature covers that. The idea of starting from scratch and finding alternative ways to play and areas one cannot get to by playing a single path is RPG territory.
Defying genre is something a lot of developers, Hell, even filmmakers and writers as a whole do, mostly because they hate the idea of being categorizes as being this "type" of story. I totally understand the feeling, and I highly doubt people go into a story saying "I'm going to write/make something that's going to be in THIS genre!" Still, knowing the genre of something does help, especially if you're in a certain mood for a particular game/movie/story.
I can't help but think of this quote from Alan Moore:
"Life isn't divided into genres. It's a horrifying, romantic, tragic, comical, science-fiction cowboy detective novel. You know, with a bit of pornography if you're lucky."
That being said, I wonder if some people literally go into games thinking about combining one genre with another. Very often I see RPG elements in a game, and a lot of games get categorized as "action/adventure" games for lack of a better description, though I know there are more games that combine other genres, though I'm not sure about what they are or how successful they were.