1. FF VI--considering the context of time that it was released, it had the mixture of a good cast, story, setting, gameplay, and villain. Everything meshed well.
The rest of the list is subject to change:
2. FF X-- Story was good and told well. I wish they would have dealt with more of the "dream" world and the origins of "sin". The "hammy" voice acting got on my nerves but I overlooked after playing for a second time. The development of Tidus and Yuna as characters was done well. I could have done without the love story.
3. FFVII-- I think the overall concept of VII was good but the execution of the storytelling could have been told better; having spin-offs (Advent Children, etc) make me believe this is especially true. The cast had decent development until disc 3. The gameplay was good. The setting, for me, helped contribute to the overall make-up of the game. If felt like I was playing a punk sci-fi game ala BladeRunner.
4. FF IV-- Story of redemption, cast, gameplay made this entry to the series a good one.
5. FF IX-- A FF with purposeful HUMOR made this entry a huge plus. I like the relationship between Steiner and Zidane. lol Everything was good except the gameplay. I thought it played slow.