Her W used to scale off AP, so it was magic based, but I can agree if they changed its damage to physical it would not be a bad idea.
Read this before you post with a calculator handy (http://leagueoflegends.wikia.com/wiki/Miss_Fortune)
I don't think you guys understand how her ultimate scales off her AD, her W skill impure shots scales with 6% of her total AD and stacks up to 5 times (6% x 5 = 30% of your AD at max stacks), and her ultimate applies up to 8 stacks of her W (so good to max W for max dps). If you understand how her W works, more stacks equals more AD per shot. having an additional AD ratio on her ultimate would cause it double dip and do insane damage on par with some the hyper carry mages that can delete individual players. Her W with 200 AD does 12/24/36/48/60- - 72/84/96 bonus AD per shot (+1 X ult rank after the double dash), if you stack somebody up then ult, that starts hurting alot alongside the base damage of her ult.
Furthermore, MIss fortune is a interesting type of ADC that could theoretically be built as hybrid (get liandra's and watch the damage her E does :P) and do a ton of damage. Her ultimate scales off AP so there would be your double dippage, while stilling scaling off AD via her W's AD scaling.