Many might think it odd to rank Final Fantasy II higher than the first and third entries in the franchise. It is true that the sequel makes use of some odd mechanics, though there are several other important elements in the game that help it rank higher than other entries.
For starters, it lays the foundation for multiple recurring themes and characters, including Cid the gruff airman, the reluctant Prince Gordon, who can also be seen as a forerunner of the bard, Prince Edward from Final Fantasy IV, and Leila, who shares similarities with Final Fantasy V's Faris.
There's also the story. This was the first Final Fantasy game to place an emphasis on story, and despite being basic -- and a bit Star Wars-y -- it's not bad, focusing as it does on political intrigue and the consequences of unbridled lust for power, toying with concepts like the importance of family and forgiveness.
The inclusion of the learning feature makes the experience a relatively deeper one as well. As the characters learn more about their world and how it operates, so do the players. Admittedly, that immersion gets thrown out the window with the leveling-up mechanic, where Final Fantasy II replaces stat increases through leveling entirely, making things like attack, evasion, and spell levels increase depending on how often they are used.