Well - for one fitness is very taxing on the body. Kelly had been at it many years, had her share of injuries, she could not exactly do it forever.
The physique round is very subjective, but the routine round is easier to discern who is 'simply better' - and Kelly was one of the best - end of story. I agree with Tre, only Stacey & Jen [however I'll add Kim Klein into that] were at Kelly's routine level.
Personally, I felt that Kelly was underscored at times.