Well, I feel its because their is a balance issue, VII and VIII both focused on concepts that most would agree is sci-fi territory, genetic engineering, super weapons, Time Travel, space travel, throw in the fact that both games feature heavy usage of modern technology like cars, guns, cell phones, satellites, helicopters and missile silos.
I feel the original VII can still be classified as fantasy/cyberpunk but VIII is a bit of a different story. It has Fantasy elements but I really feel its genre is much closer to Sci-Fi especially since Sci-Fi has changed so much in the last 20 years. All the games hit both sides, I feel the main difference is a balance of said ratios. I feel most of the FFs generally hit a 50/50 mark V, VI, VII, IX, and X are all just as much traditional fantasy as they are science fiction stories.
My personal taste? I, IV and V are sorta a perfect 50/50 mix of sci-fi and fantasy. II and III are the closest to being traditional fantasy in the series. VI is Steampunk which is easily one of my favorite niche genres, VII has a pretty good steam/cyber punk feel, IX is a good mix of hardcore Jim Henson style fantasy (more Dark Crystal and Labyrinth) but its hard to deny its heavy use of sci-fi elements as well. X is fantasy done with a Japanese mythos. Its story is actually a retelling of one of the oldest legends in Shinto. Though I actually like Oriental Fantasy, I don't particularly care for X's style cause its relatively "safe". XI is more in line of "Old school FF" and XII is quite more difficult to pin down. I'm beginning to feel Ivalice and all its incarnations deserve their won damn category of fantasy.
Of the main series, I feel III and IV represent the best fantasy "feel" to me. Though I would rank XII as the best if I counted all the other games from Ivalice.