Civ II was more fun, and there is more negative about the game than positive, but since you asked. . .
Besides graphics, the GOOD parts of Civ III are resources (even though we have to Edit their number up), unique units, the queue thing in city production, city governors are a little more helpful, and I like being able to establish embassies without marching a diplomat to their capital even though I miss diplomats and spies for espionage stuff. I also like the idea of Small Wonders a lot.
Borders in concept is good, but not culture borders which many hate.