I agree that there are some missing stages. There is a good deal that is out of place or illogically arranged in the tech chart.
However, though some folks are quick to point out that CIV is just a game for fun and not education, it is also a simulation game, simulating history and the path of technology thereof.
In that vein, cannon should be a few stages before riflemen, and if there is an agricultural revolution to add in, it should appear before or during the Rennaisance Era. It should be a tech and not an era.
Of course, and here I do digress a bit, some of the earliest civilizations were extemely advanced, like the Sumerian, the Egyptian, and the Chinese. They were on a path beyond other peoples.
Therefore, in the same way that a player can only build certain units with certain resources, I think the next Civilization game should seriously experiment with tech advancement choices being dependant on resource acquisitions to some extent. I don't advocate plague or famine random events only because there have been human-engineered famines by the Russians and British respectively, independant of nature. But in getting back to my point about resource+tech, can you have an Agricultural Revolution without horse and iron resources?
This might not solve a lot of issues on the tech tree, but it would steer this simulation a bit more on course.