I like both types of RPGs equally. I also like the idea of mixing fantasy and sci-fi into one game universe. I liked the Cyberpunk setting of Final Fantasy 7 and 8, because it broke away from the traditional fantasy setting and included fantasy elements in a largely sci-fi universe. The Steampunk setting of Final Fantasy 6 was pretty awesome too. It looks like FF13 will go back to Cyberpunk, but the fantasy elements will be more obvious. This, I like.
I know I've only mentioned Final Fantasy so far, but don't get the wrong idea. I'm NOT a fanboy, I'm just using the FF games as an example of how RPGs can mix sci-fi and fantasy into a formula that works nicely. Trust me, there's a long list of other RPGs that I love. I'm currently playing Mass Effect 2, having imported my data from the first game. So far, the entire game is made of win. And now that I've actually experienced mineral scanning, let me say this: It's not the best part of the game, but people are making it out to be worse than it actually is.