Syndicate Wars improved on the original in almost every aspect. The most obvious was the shift to a fully 3D destructible city. The old game suffered in hiding what was going on behind tall buildings, and still the new 3D view did not compensate fully for this because it would still be frustrating to keep panning the camera to obtain a good view of the action, while running around houses and slugging it out with the acolytes of the Church of the New Epoch.
The game structure and missions remain the same, as does most of the research and weapons trees, with some minor improvements. The main difference of the campaign is that you are fighting one enemy, rather than multiple rival syndicates. Vehicle variety has also been improved a lot, and now also includes flyers. The game is also quite hard compared to the original. Whereas in the old game, hiding behind a corner with your flame throwers ready was an effective strategy, you really have to keep moving in this one.
I personally didn't like the change to the weapons interface, in that ammunition was changed to a global energy bar, from which all weapons drain their power. So while weapons won't run out of ammo, you'll still be able to drain all your weapon energy with your most demanding weapons, leaving you virtually defenseless for a while. All in all though, this is a great sequel, and a joy to play.