If all of art is subjective, then what good are critics. Why should their opinions get published and not yours. As you say, in most cases there are clear distinctions between your list of favourite films (or films you consider to be the best) and other critics polled lists and the question is why is there such a huge difference? Now you're asking if there exists an objective criterion for determining what films are genuine great and what films are just personal favourites. I think that any attempt at developing such an objective criterion for judging films is both futile and self-defeating. It discards the most sacred feature of cinema, its ability to speak to everyone differently. One is defined by one's biases and I see no purpose in judging a film from an unbiased perspective (if such a thing is even possible).
I would think it's because the people who made it their life's work to deepen their understanding of the art form are the closest to an authority on the subject (though not necessarily so) and earn more of the right to have their opinions considered (if not necessarily agreed with). The guy who sees maybe one blockbuster a year is as entitled to his cinematic opinions as Roger Ebert, but there's still a significant difference between the two.
Let me give you 2 examples to illustrate what I'm saying. For instance Francis Ford Coppola's Apocalypse Now is widely regarded as not only one of the great war films of all time but one of the greatest films, period. Now although I can admire its technical virtuosity, its beautiful visuals and its narrative ambition, from a philosophical point of view, I think it's a big bag of hooey. It seems to have a lot on its mind with regards to the corruptibility of men in the face of war, about men becoming killers and so on but it doesn't know how to say any of it. It's 3 hours of preaching with no justification or truth behind any of it. Also if Coppola wants to examine the subject of war honestly, I don't think he can do it with by starting with a preconceived notion of war being the worst thing that's ever happened to human beings. Don't get me wrong, I'm completely anti-war and I'm very saddened when I see footage of what's going on in Iraq and Syria today but these grand claims of war being very unnatural and having fundamentally political origins are largely unfounded. Our entire history as a species has been entirely defined by wars so Coppola's statement about "war corrupting man" is the sort of pseudo-intellectual drivel that fills the books of Pharaoh's magicians. Does he really think humanity conquered the earth whilst suppressing all other species, by being loving & caring? War is at the heart of evolution, natural selection at its absolute pure. I've always hated it when film-makers pretend to be philosophers without having anything meaningful to say. This is a subject matter that requires a certain level of intellectual maturity that lacks in Coppola.
Clearly I already had strong opinions on the subject matter before I saw the film and perhaps if I didn't have any I might have enjoyed it more. So one could say that it's not the film's fault, because in both cases the film was the same, it's about the thoughts I bring with me. But I think this point of view is about as unhelpful as it gets. I think the fact that I personally feel a certain way about this subject defines me as a viewer so the fact that I completely despise how the film explores its ideas is indeed a valid criticism of the film from my point of view which is all that matters to me.
I wonder what you do think is the worst thing that ever happened to human beings if not war. Even assuming it wasn't, I don't think that necessarily makes it good enough that a strongly anti-war film like
Apocalypse Now automatically looks stupid for saying it's bad.
Anyway, I was under the impression that
Apocalypse Now agreed with the idea that humanity is already inherently warlike, but it also balanced it by saying that humanity was also capable of seemingly irreconcilable levels of love and compassion at the same time (as emphasised by Kurtz's monologue about the soldiers who could cut off children's arms before going home to their own families). It gets more complicated than vacuous "war is bad" moralising - if "war is at the heart of evolution" then the film chronicles a de-evolution as it progresses backwards in time (figuratively) and deeper into the heart of darkness from the generals' neat and pleasant office to the corpse-strewn Kurtz compound.
But yeah, this is the kind of stuff you can miss if you let strong opinions override your ability to judge the film on its own terms, but I guess that might well be true of all of us.