It's the same system, for the most part. I think things are on a smaller scale, that's about it. I've played them both, and it was definately simpler to make a character for d20 Modern than for D&D, that's for sure. I'm going to have my campaign be mostly realistic, so there isn't going to be any mucking around with spells and such, so I'm going to have a modify the rules and potential classes a bit.
Plus, I prefer a sci-fi setting to a fantasy one.