I just re-installed Empire Earth II, and bought Rise of Nations because it was relatively cheap and I had pretty good childhood memories of it. In both games I played two matches, and I got to admit that the Rise of Nations playthroughs were much more enjoyable. In Rise of Nations it was really fun to see your villages and cities drastically change each time you reach a new epoch. In Empire Earth II on the other hand, it rarely changed. In Empire Earth II, researching new technologies felt like a burden and very linear to me. In Rise of Nations, you can research on all kinds of different areas; Military, Economic, Political, Science, and another one which I forgot. Yes, this also applies to Empire Earth. However, the connections between the technologies and the area you are researching in makes little to no sense, completely neglecting the fact that some players want to be a prosperous peaceful civilization, establishing trade routes all over the world, paying other civilizations to do work for you. In Rise of Nations, you had so much more variety in upgrading or making choices, you could choose to be a religious civilization, a monarchy or republic, etc etc.
I don't really see anything on Empire Earth's part that is better than Rise of Nations to be honest. Maybe the silly futuristic technology in the last couple of epochs; other than that, nope. I am posting some screenies tho of my Empire Earth II playthrough.