A couple of reviewers have referred to this film as twaddle, and that to enjoy it you have to have had your brain melted from actual thought. Another reviewer has detailed the film's allegory, which is fair enough, but then allegory is what you go to church for, not why you buy a movie. Although I speak for myself. Who knows.
The thing is, El Topo is less like a movie, or even an art film. It's more an insanely theatrical hallucination. There are no recognisable human beings in it - as in, no-one behaves in a manner you have witnessed in real life. It is deadly serious, and then there's lowbrow hijinks. There's lots of mime in it. The first line of dialogue, which is a long time coming, is "I am God." And there's some weird violence - the first sequence ends with a naked child killing an old man with a gun. So, you know, I'm just saying.
But it is incomparable, which is why people get so upset. If there's a genre frame, it's the revenge western - but even then, you know, not really. And yes, it is pretentious. But not in a French relationship-drama way; more in a "I do not know what is happening but it appears to mean something" way. Which can be frustrating. But then, you shouldn't only eat hamburgers. Vary your diet.