Okay, putting Monster Hunter aside for a moment, lets consider what would make a JRPG better.

Effort Values.

You see Pokemon is actually pretty deep. When you fight different pokemon, and beat them, they give your pokemon a EV point or two in a certain stat.

For every 4 you get you get 1 point added to your stat.

Basically, I'd like to see an RPG that lets you build a squad that gets stronger based on the sort of enemies they fight.

It makes grinding interesting.

Maybe add to that a Blue mage style skill system. The party learns abilites and skills from the enemies they fight.

Quests and Story give you points in class based system. An overall direction of growth.

The world would be open for exploration from the start, and one would have to be careful where they go and what enemies they fight/questlines to follow.

Now THAT would be a great RPG to play! :D

This is a great idea.
I like very much the game okami. Its a japanese action adventure (I call it the zelda of the playstation, in a positive sense). There you are a sun goddes in shape of a wolf and the world has been destroyed by some ancient evil. Your goal is to restore the world. You get exp (its called luck? or happiness?) for helping people or animals and restoring corrupted environment but NOT for killing enemies.

You take a kilogram of WoW and mix it up with 350 grams of Skyrim, and you'd have a winner.

... WoW's world with Skyrim's style (first person perspective RPG). That would be so awesome.

Not sure if it's quite ultimate, but the one I'd like to see would be like:

Set in true medieval europe. Holy roman empire, byzantines, papal states, moors, stuff like that.

No magic at all. Superstition aplenty, but no spells or effects. Just swords, axes and such.

Really meaningful, hard choices. Like.. what if being greedy and asking for more would actually.. like... give you more! Where being a saint would mean you just can't afford that plate armor.

No zombies, no monsters, no nothing like that. Just us people being wolfs to people, just like wolves don't.

Ability to ferk up your game by making the mentioned hard choices. Making the choices important. If you end up with no money, gear, allies or usable skills then that's just way bad. Like.. don't expect to win in Civilization if you just build a happy city by spending everything on luxuries and not expanding at all.

Ability to solve everything by multiple means. Maybe you're the toughest, meanest fighter around, maybe you're a moneymaking genious and hire such fighter. Maybe you just talk everybodys ears off, or seduce them.

Heaps of gender inequality, racism and pure greed from even the good guys. Not the usual 21'st century utopia of an ideal society set in semi-ahistoric background.

And some kind of plot would be nice.