> It does fall faster, if you drop both stones in the atmosphere; the heavier stone has more mass per unit of surface area, to better overcome a constant level of air resistance.

Not necessarily; for one thing, if the masses of the two stones are not significantly different, the difference in the effects of air resistance would be unmeasurable given the instruments of the day.

For another, the shapes of the stones are important. One with a much greater sectional density, oriented correctly, could fall faster than the other, even if it were lighter.

But that's just nitpicking. If I remember correctly, Galileo used inclined planes because there were only imprecise water clocks available to measure the passage of time. His choice of apparatus was brilliant :)