OK. So we've established that Aeris ends up as the final ingredient to Soup Dude's culinary masterpiece. It all makes sense now.
When Cloud and Aeris first encounter "The Dude" at Wall Market. His soup was incomplete, hence why he was unwilling to share. He was missing the one final ingredient that would make it suitable for consumption. Little did Aeris know at the time, as she savoured the gentle aroma of the bubbling cauldron, that she would be the final piece of the puzzle.
In conclusion, Soup Dude is a sick bastard that likes cooking flower girls in soup and dust. Only one question remains... how did Aeris' body end up back in Wall Market after being left at the City of the Ancients?