I think a lot of it is perception. When guys who are used to 10's switch to 9's they usually hate it right off the bat. Is it really fair to compare when IMHO you should probably raise your action a slight amount for the 9's and give them a chance to break in. I feel that 9's with medium action can sound as good as 10's with low action.
Sometimes our ears play tricks on us. Can you hear a difference on clips between string gauge? Or let someone else play 2 different guitars, that sound close to begin with, using different string gauge and see if they are really that different.
All i know is EVH used 9's tuned down the Eb on the first VH album and that's the best tone ever. Me personally, i would use 10's on a Les Paul or similiar Gibson, and i now favor 9's with superstrats and FLoyd equiped guitars. For me, it's a feel thing.