FotS has a truckload of new stuff and fancy eyecandy and units, while RotS (imo) has better actual gameplay (talking about battles here, campaigns are really the same anyways).

What annoys me about RotS is a huge lack of diverse units, some of which FotS has too many (like 1794567 different kinds of line infantry, where 5-6 probably would have gotten the whole hey, we have guns now =D thing across).