Travis,
Having a master's degree in History of Science, and having taught introductory astrophysics with a strong historical approach over the past 20 years, I found your essay particularly interesting. The two case studies that you present, Ptolemy vs Copernicus and Dalton vs Avogadro, are well chosen, and well explained.
To teach a controversy well, to go beyond just saying "there was a controversy and it was resolved", you need to go into the details: for example, as you indicate, you need to appreciate the fact that, in Ptolemy's theory, the motion of each planet on its major epicycle is "locked" to the Sun, a fact that was "pointing" toward Copernicus' solution that the planets revolve around the Sun.
And that's where it gets... challenging. Even though I teach to fairly bright and motivated students that want to pursue careers in science, I have found that it is difficult to motivate them to care about the subtle nuances that are critical to fully appreciate scientific controversies. Most students want ready made answers, so they can "pass the test" and get their diploma. They believe it is already so much work to get "up to date" with current science, that they shouldn't have to be forced to ponder the meanders of history.
Of course, it doesn't mean we must give up on using history of science as a way to teach science, but it explains why this approach is not more widespread. On the bright side, there is a tendency in the teaching world to shift the focus from "rote" knowledge to "learning how to learn", and the teaching of science through scientific controversies fits well with this new way of doing things.
In my essay, I have taken a "complementary" approach to yours. I propose that we can teach science better by "projecting into the future" -- by focusing on the issues that are the most important to the future of humanity: I call this approach the Futurocentric Education Initiative. But, as I say in my essay, it does not mean that history is eliminated: if you can motivate a student to acquire skills and knowledge that is important to the future, you can then explain the importance of knowing about the past aspects of this subject -- and I think that scientific controversies offer invaluable learning opportunities in that respect.
I have looked at all the essays, and read more than half of them from start to finish. Your essay is part of the short list that I hope will make it to the finals, and I have rated it accordingly. If you have time to look at my essay, rate it and comment on it, it would be quite appreciated.
Good luck in the contest!
Marc