Personally, I'm about 120 hours into Xenoblade and nearing what I assume is the last stages of the story. I absolutely love the game, and feel it's probably my favorite RPG of all time. There is little I would change about it, but some things I would keep or improve given the new hardware:
-A new, weird setting, just like the first game. The two titans is one of the coolest settings I've ever seen in a game. Do it again, Mono!
-Vast, beautiful zones. Also, keep them colorful.
-HD visuals with more realism and improved lighting. That doesn't mean I don't want color and variety and "alien feel" to different zones, but just higher quality.
-Touchscreen control of secondary characters. I want to control the whole party.
-Vehicles.
-Another fantastic story.
-Another endless supply of side quests.
-Lots of exploration.
-Another great soundtrack.
-All new characters and cultures.
I really would prefer an all new story, like final fantasy does, and a new setting. I think that's the only way you can get that feeling of 'awe' from an all new world.