A few things:
1. Longer timeline.
2. Removing the weird religion mechanics.
3. Realistic government models for the Romans (there were two consuls a year for one), and you could even throw in the Spartan dual monarchy.
4. A larger map (not just larger, but with more regions included in areas such as Italy, Greece, and the Mid-East.
5. War goals with the new casus belli system.
I'm sure I could think of more, but I must admit it's been a while since I've loaded EU:R up.
Spartan dual monarchy? Now I'm interested.