Final Fantasy VIII and Final Fantasy X both saw SQUARE taking a number of risks, many of which paid off, if you look at it simply from the gameplay design perspective.
Both Final Fantasy VIII and Final Fantasy X featured innovative character development systems that left flexibility and control in the hands of the player. The Sphere Grid and the Junction systems had similar functions: that is, to give players control of to develop their characters as they saw fit, although the end result were different in that characters in Final Fantasy X gained permanent ability with growth, whereas gaining additional levels held few benefits for Final Fantasy VIII characters, since growth from leveling was minuscule at best; if anything, the two games are completely opposites of one another in terms of gameplay, in that Final Fantasy X encourages grinding to allow players to further customize their characters, while Final Fantasy VIII puts little stock in grinding, since character attributes and abilities are based on something outside of leveling. However, Final Fantasy X was better received than Final Fantasy VIII in terms of gameplay, something I attribute to characters learning permanent abilties, which gave players more flexibility than Final Fantasy VIII's Junction system, where many players were somewhat limited to how characters could develop, dependent on the abilities they had unlocked for Junctioning.
SQUARE isn't particularly good at making direct sequels; that is my belief. Aside from Final Fantasy X-2, which saw SQUARE's abandonment of the deeply customizable Sphere Grid, hot-swapping turn-based system and jumping to the old ATB system and a comparatively shallow Dress Sphere Grid system, Final Fantasy Tactics A2 is another example of this. Although SQUARE kept most of the good aspects of Final Fantasy Tactics Advance in making its sequel, the developers also removed the Law system, the only system in the game that made the game interesting and different within the genre; although the system wasn't removed per se, it was effectively nullified when it became of no consequence, allowing players to completely ignore it without any penalty of note. Likewise, the Auction system added to the game was no more than a gimmick and was effectively superfluous, as it added no value to the game's core system.
Of all the direct sequels SQUARE is responsible for, the only titles I can honestly call good are limited to Parasite Eve 2 and Chrono Cross, both titles that saw major changes to the game compared to their predecessor; at that, Parasite Eve 2's gameplay was bit of a clone of Resident Evil with role-playing elements, and Chrono Cross was very much a clusterfuck that saw the developers introduce too many extraneous characters and thus never really fully developing any of them as truly unique playable characters the way characters in Chrono Trigger were all distinctive in function.