I would LOVE for the Mass-Produced Faces to be Smash Run enemies, as well as those floating Mechon that Jade Face summons when you fight him for the last time. That one Mechon with the tentacles would be pretty interesting; instead of performing generic attacks, it could grab players from far away, pull them into the ground, and throw them. The Telethia would be interesting as well, particularly the giant floating fish-like one you encounter late in the game.
For an assist trophy, it would be funny if the Colonel would pop up and start lecturing you--he could be a more dangerous version of Mr. Resetti.
Melia, in mine opinion, would definitely make an interesting Assist Trophy. She could use either her Mind Blast attack, in which she discharges a powerful surge of magick from her hand that expands as it travels, or her Shadow Stitch spell, which binds nearby opponents, making them completely unable to move.
Oh, and Guar Plains is a stage on the 3DS version as well. If you look closely in the below image, you can make out Mechonis's Sword.
I bet that there are more Xenoblade tracks. I have a tough time believing that we will just get three tracks from Xenoblade. I bet that One Who Gets in Our Way is one of them.
Personally, I am hoping for Prologue B. That one has got to be mine favourite. Oh, and The Night Before the Decisive Battle.