My experience has been that EMGs are great for pure metal in some guitars. In other guitars they don't respond as well at all and can sound cold and brittle. You have to try them and see, but the odds are generally about 50-50 on whether the'll respond well in any given guitar.  Personally, I see them as a sort of a one-trick-pony pup.  In the right guitar, they do what they do very well.

Duncan pups are always gonna be more versatile and more forgiving in just about any guitar. And they make some pretty hot pups, but you'll probably need a bit more gain at the amp or from a pedal than you will with EMGs.  However, if you find yourself in a situation where you're not always playing flat-out metal (like at a jam), the Duncans will still respond favorably where the EMGs might be out of their element.

So it really depends on your situation.  If I were gonna have only one guitar, I personally wouldn't choose EMGs.  However, I since have several guitars, it's great having one of them set up just for metal, with EMGs and a Floyd Rose.  But it's a specific tool for a specific job.