Trials of Mana. Actually the whole Mana series were completely unique and very innovative when they first released. But the combination of story telling, party building, and combat system still hasn't been topped for me. The games are something I always have ready to emulate at all times. Fingers crossed they decide to remake the rest of the Mana series. Legend of Mana needs some love even though I remember most people weren't really keen on building their own world.

The Tales series was probably the closest before the switched from 2D to 3D. The switch, I thought, took away a lot of what made them stand out from other jrpgs in the market.

My close 2nd is Legend of Dragoon since it actually changed the combat system in a really meaningful way. Legend of Legaia also did something similar but I thought the storytelling was better in Legend of Dragoon.

Soul Sacrifice still needs some love. It's only downfall was releasing on such a niche system like the Vita. It actually moves the MH formula forward in a really interesting manner by forcing you to make really interesting choices in the story.