I like both of them too. I like most military films and I've always liked any movies about the Khan's.
In my opinion, 'The Conqueror' is a highly entertaining film, with hugh production values, a wonderful music score (by none other than Victor Young), and excellent character actors. And besides all this, the out-of-print Goodtimes DVD spots a wonderful transfer and carries the original 2.0 stereo soundtrack, which really booms out of your speakers.
I can certainly think of a dozen other Duke films that I'd pass on to watch this one.