Don't get me wrong, I can see why so many people Master of Puppets, because there is really nothing wrong with it at all. To me though, I just find it boring for the most part. It's not a very exciting album I don't think. I think Kill Em All is packed with energy and killer riffs and attitude, Lightning has that attitude/energy but combined with better songs, Justice has great songs and structures and melodies and stuff, and the Black album has awesome production and great focus on catchy songwriting, and again lots of awesome riffs. But Puppets to me kinda lacks the energy/excitement of the early ones and doesn't have the songs or melody of Justice or the songwriting and catchiness and huge sound of Black.
I really can't put my finger on why I don't like Puppets, it just doesn't appeal to me. I think what I said above is the best way to explain it, its just lacking the things I like about the other albums.