I'm calling this "extensive" rather than "complete" because it's entirely possible I missed some. However, I think I got the bulk of them down. Just a few general (and one or two cracky) things to start off (non-spoilers, unless you haven't seen any of the trailers):
The way music is used has been changed, sometimes for the better, and sometimes not. On the whole, the music has been dropped further into the background, so the sound effects (weapons clanging, people grunting, etc.) are clearer. That's a plus, but I found I missed the volume and energy in some of the fight scenes.
While the remnants pretty much survive fight scenes without getting dirty or bloody, the rest of the characters are no longer so fortunate.
Loz provides his own sound effects. When he fires his motorcycle machine gun, he yells the equivalent of "rattatattatatta". I'm also pretty sure he says, "VROOM!" when he guns his motorcycle down that cliff at the beginning of the movie. (It doesn't show in the subs, unlike his machine gun noise, but it sounds like he does it to me.)
Masamune now has its very own sound effect. It makes a sort of metallic hum all the time.
Voice acting for Marlene, Denzel and Moogle Girl is very good. I think I still prefer the original Marlene, but I don't have any complaints about the new one (I'm just used to the old).
( On to the serious changes! )