Well as posted earlier, everything is the same, almost.
Still I consider it a greater challenge than X-COM UFO Defence (enemy unknown).
Maps are almost always bigger and with more obstacles. The research tree has been modified to be more complex, and not so obvious. There are new races to fight, among those the evil lobstermen.
Well, if you like X-Com UFO Defence then you'll probably want to finish this game off too.
Check for Kuo-Sheng
Kasey Changs for more information. It covers the most of the game and is a great source of information.