Ever play FF4? It's a classic, fantastic game, yet the end boss, Zemus, isn't even mentioned until the last dungeon and suddenly becomes the boss of the game. It's called a twist, even if it was out of place.

FF9 was essentially a combonation of all the previous FF games, most elements of the story are DIRECTLY derived from the previous games, and FF4 is no exception; the Kuja / Zidane connection is parallel to the Golbez / Cecil connection, and Kuja fills in Golbez's role in the latter part of the game (he took on a Kefka role in the early part of the game, serving under the emperess and her male and female generals, ala FF6 with Leo and Celes, but instead Steiner and Beatrix). So the end boss is in the style of Zemus, and considering the space elements that are in FF4 the connection is pretty clear.

FF9 is mostly disliked because people don't understand it at all, the style and the many, MANY references contained within; people who started Final Fantasy with FF7 (which are most players) wouldn't hit on all the classic references and allusions, and they are the things which help make the game great. It is a more solid and better game than FF7 (which lacked focus and direction), and deserves a lot more praise than it gets.

The boss thing and the other references were very clever, it just goes right over the heads of a lot of people; it's not really a game for the masses of common RPGers who think that 7 is the 'best game evar', it's more for the advanced players who would know what they are looking at when they fight an Antlion boss or hear the Gulag Volcano theme

7

FF7.