As someone who's never played a FF game and is just going by what I hear about from the fanbase, I had no idea VI was considered to be such a classic. It got #2 on both IGN's and GI's lists. It's always VII this, VII that with the fanbase, with some VIII and IX sprinkled in (from my inexperienced, outsider point of view). Just find it surprising, is all.
From my experience with the Final Fantasy fanbase the usual popularity order I've seen is VII, X, VIII, IX, VI and IV. I feel over the years XII has pushed itself back into the top 5 but my experience for most of them is it was always the most disliked.
Gaming sites it's very different. The order I generally see online is VII, VI, IX, XII and VIII with some vocal IV and XIII fans here and there.