This is an interesting comparison. I think it would be almost as interesting to compare Phantom of the Opera and The Four Horsemen as the epic tracks from both albums, since that's where my mind almost immediately went when I started thinking about these albums.
I used to really not like Kill 'Em All. Thrash isn't exactly my thing, I don't like the immature party/drug/senseless violence lyrics that are on most of the songs (really all of them except The Four Horsemen, Jump in the Fire, and, obviously, Anesthesia). It has actually grown on me the last few years as I've come to recognize that even then Hetfield (and, fine, Mustaine) had a strong sense for catchy riffs and melody. I think that sense is wasted more than it ought to have been on thrash headbangers' anthems, but I can't deny Seek and Destroy or Metal Militia as precursors to the material I really love that was to come.
Iron Maiden also has some lyrics that I don't care for—Prowler, Charlotte, and really Iron Maiden, too, when it comes right down to it, although I'm kind of immune to that one after having heard the song 1,800 times. It also does not have Bruce Dickinson or Adrian Smith, and unlike Blaze Bayley, Paul Di'Anno does not do much for me. But Phantom of the Opera is far and away the best song on either album, and I think Remember Tomorrow beats The Four Horsemen for #2 (incidentally, that's the only song where I am particularly enamored of Di'Anno's performance).
I came in here expecting to go straight for Maiden on the principle that I prefer them out of the two bands (though I love both) and that I have bigger problems with KEA (don't like thrash much, dislike the lyrics more). But it's closer than I thought it would be. Overall, though, on the strength of Phantom of the Opera and Remember Tomorrow, I think I still give a slight edge to IM.