"This is easily disproved by dropping a heavy object and a light object of the same shape from a high place and seeing which hit the ground first. Yet it took over a thousand years before anyone thought to try this experiment."
Not to be too pedantic about it, but the reason the belief survived for so long is precisely because it isn't easily disproved. If you drop a heavy object and a light object of the same size from a high place, the heavy one will absolutely hit the ground first. (Try it!)
Galileo disproved the Aristotelian idea that heavy objects fall faster with a thought experiment, not through physical experiments and data collection.
He used deductive rather than inductive reasoning. That's why it was a proof.
As well, given two rocks of similar density but different mass (assuming m*g >> F_d for both) it generally takes a pretty high place (that is: higher than the couple stories that they had access to) for differences in acceleration or V_t to matter enough that ancient Greeks would have actually noticed.
A = projected area, which is the same if our objects are the "same shape".
As for the rocks, you're applying benefit of hindsight. Say I show you a balloon filled with air and a balloon filled with water falling at obviously different speeds. Now, you have to explain that with this odd theory of "everything falls at the same speed" -- not the other way around. In the real world, it is evidently true that heavier objects fall slower, and any better theory that disagrees must explain this (e.g., posit the existence of air resistance) before its new predictions matter.
Not to be too pedantic about it, but the reason the belief survived for so long is precisely because it isn't easily disproved. If you drop a heavy object and a light object of the same size from a high place, the heavy one will absolutely hit the ground first. (Try it!)
To see that this must be the case, imagine that they hit terminal velocity. (Formula for this is at http://upload.wikimedia.org/math/2/2/2/222c90eb77c221a2c6b10...) All variables but m are the same in each case.
To get the "right" result, you have to be fairly thoughtful (e.g., put dense balls on an inclined plane).