Skies of Arcadia, the combat isn't the greatest and it can also be pretty easy but the sheer depth of the world and the whole exploration aspect and the boat battles and the scale of the game are excellent.
Further back, Ogre Battle 64 or Harvest Moon 64 if you count them, and finally Super Mario RPG even though its really simple in nature I loved the style and it had such a great cast and even a little emotional depth to it.
I just never got that out of CT, like when Chrono 'dies' and comes back it felt like "Oh crap Chrono is gone now how are we going to complete our quest." and "Oh good Chrono is back now we can continue our quest." I played the game the whole way through once (not that long ago either) and it just felt hollow and not a lot of it even stuck with me. The only really memorable point (storywise) was when the Robot enters the robot factory and ends up being attacked by his brothers, that was actually pretty interesting. I know nowadays we have a lot more ways to storytell give a visual experience, but even for the time I don't feel like the writing adequately conveyed much of anything in the limited opportunities the story presented.
