IX is under appreciated because it brings back themes of the Originals. (FFI-VI) In this game, people would find it very hard to get 9,999 HP unlike FFVII-X, where all you had to do was equip Materia, Junctions, and go through tons of HP nodes. Again, in FFIX, it is very hard, and quite possibly impossible to get 9,999 HP. (I saw a picture of everyone's stats at lvl 99, none of them were 9,999?)

Another theme it brings back is being able to use four characters in battle instead of three. Though you did have more party members, the battles weren't too easy where all you had to do was just mash "Attack" like in, say FFVII.

Also, the final boss of the game, Necron, speaks of words much similar to that of a villain in another FF. The Iifa Tree is also a connection to a past FF villain as well; Grand Cross is a a connection to that same villain.

Yes, the most likely reason for it being under appreciated is because it has a different theme than the two previous ones before it VII and VIII. They had more of a "futuristic" theme than FFIX. Many people probably just weren't used to playing FFIX because it was different to them and much like Originals.

In my opinion, IX is the best of Second Generation FF's and X is the second best of them.