Yea, that scene was a lot cooler. But it made for some inconsistencies with his clothes, seeing as when he's floating in the water all the cuts are gone. Also, when Aeris and Zack are talking to him after the explodey bit, the cuts from Sephiroth are there, but the bullet hole isn't.
I was kinda hoping they would fix the part where one of Cloud's blades goes through the hilt. When he's standing on the sword on the side of the building and kicks it down to make the blade come up, it goes right through the hilt, very annoying like.