The first FF game to really throw a radical change into the gameplay style was either 8 or 10, the latter it seems being the last one I hear talked about as a mainstream popular game. Also, Final Fantasy has dozens of games and spin-offs as well, so seeing changes take place was inevitable. And even if the games sold well, there's no denying that there were a lot of rough patches with the game design in the PS2 era onward: FFXII was a huge open world game, then XIII became ridiculously linear and narrative focused, and both games were among the most radical departures from the turn-based systems the previous main games and even some spin-offs used for their battle system. While 12 and 13 all have their fans, it's rare to find even fans of the game that won't have some kind of complaint about the design: one big let's player I know even says that while he likes the game, he can't recommend it because the issues he personally takes with it are objective design issues that might bother others more than him.
Pokemon is obviously having trouble with the opposite trap, potential stagnation, but I think the main reason we're calling it out in this case is because Gen 5 showed they CAN do something to mix things up, but then returned to something "safe" to get the 3DS some momentum and get a feel for the jump to 3D main series games, and even then there are hiccups (blandest cast in a while, the engine is poorly optimized for battle, and while the model QUALITY is good, the designs in many cases leave something to be desired).
One idea that does interest me that Pokemon could do (and indeed was a subject of half-joking comparison) is what Fire Emblem Fates is doing: One version is for "traditional" players and the other is where they try to change things a bit more from the norm. While I take issue with it in FE: Fates case because that game is mainly doing that for story purposes rather than gameplay changes, I could see that working for Pokemon. One version has the traditional "become the champion" focus for the plot, the other could, for example, focus more on your player fighting the crime syndicate for the narrative, because it's not like the player character in the main games logically could interfere in every single one of their schemes while on their journey.
Both games would likely include the same elements in regards to the Gyms, but in the latter version, maybe the Gyms could be more of a sidequest as could the "Rockets" in the former: one issue I take with Pokemon's narrative in most games is that the Team is always stopped at the 80% mark as the climax, and that makes the Elite 4 feel more like a formality after. Gen 1 did a bit better about it by having Giovanni as the last Gym Leader, tying the end of both plots together a bit better, but every other game either the team was such a non-threat/presence that their plot felt pointless (Gen 2), or the legendary battle was the obvious climax of the main story and the last gyms felt kind of meh. Only exception is Gen 5 where the team and the gym plots were melded more, and even then imperfectly.