A Firaxian has reported that the game engine began as the SMAC engine, but is now 90% new (in the Why Civ-Specific Units are a Good Idea thread).
We essentially discuss games rules and presentation here. Besides increases in speed and customization (mod) ability (I hope) what other improvements may be visible to us?
The new game engine allows for the application of limiting resources, something that is key to Civ3 being more realistic and fun. Over-simplification of resources was fine for the first 3 civ games (SMAC too) but now the game needs more refinement to the economic system and its effect on politics, something that the resources allow, whether by trade or conquest.