The big change is the battle system, which mandates no more than one combat unit per tile. From what I recall, the AI wasn't very good at maneuvering its units, and it was pretty easy to set up defensive bottlenecks to destroy the opposition.

I've always found this article very interesting in debating the game's faults.

However,since you already have it, give it a shot! It can be fun. Maritime city-states are a gamebreaker.