While I agree the franchise is about reinventing itself, I would argue the Junction System was a rather big departure from other games in the franchise. The Materia system itself is just a further breakdown from VI's Relic/Esper/Class system which in itself is a variation of FFV's Job Class system. Most of the Post-FFV customization systems are generally just a re-imagining of V's Job Class system, IX and XIII being the exceptions to the rule.

I feel the fact VIII decided to get rid of Armor and meaningful weapon upgrades in exchange of integrating it into the Junction system was a pretty big departure. There really wasn't a game before that tried it. While spells are still limited, technically the ability to draw and simul-cast meant it was possible to have infinite spells in some battles, and the way it integrated with customization, many players found themselves to stock up on spells to use as makeshift armor and buffers for stats. You still equip Skills through the GFs but VIII makes it far more limiting, at first but then you also get the ability to remove them and replace them. Making them technically more flexible than V-VII's systems. The shear fact they introduced a "steal spell" mechanic in itself was pretty interesting and has never really been done since which is a shame because I feel it could be expanded into something cool. The leveling system itself also brought in some major new dynamics to the game that most gamers at the time took for granted. Not many games punish you for gaining levels.