I notice that practically nobody has actually explained WHY they prefer one song or another. So I'm going to go ahead and dissect them.
Guitar-wise, Flash of the Blade is one of the most simplistic songs Iron Maiden has ever done. Even the solo bits are basically two different melody lines; the first one is an extremely cool tradeoff, but doesn't make up for the fact that this song is completely formulaic and, aside from the bass under the lead break, lacks any sort of change in the structure.
The Duellists, now that I think about it, runs on the same model for much of the song. The initial lead bit, from about two minutes in to 2:50, is very similar to Flash of the Blade in that it's just a few melody lines repeated; then after the virtuosic solo, they repeat that part. The riffwork, too, is really simple. However, it's structurally much better done, as they give the repetitive lead parts a lot more room to build on each other. Also, the breakdown at 4:38 is a great way of changing things up.
The vocals are brilliant on both, of course, this being Bruce Dickinson at his peak. The choral melodies, the natural highpoint of both songs, are better in Flash of the Blade; they both have very quickly sung verses, but Duellists has more melody and sticks to the "triumphant" feel instead of the angrier bit of Flash. The consistency improves the song.
So, The Duellists. However, they're both very good examples of the Stained Class formula.