I didn't experience this personally at the time, but when I heard how Team Rocket's characters had changed in the Black and White anime, I was really surprised and spent a lot of time on Bulbapedia reading up on events (I hadn't really seen any of the show since mid-Sinnoh). I couldn't believe they weren't blasting off anymore, or that they'd had those black uniforms, or that Wobuffet of all Pokemon got left behind.
A couple years later, I stumbled on one of the XY openings at random, and seeing them in-character, with Wobbufet in tow, getting blasted by Pikachu, made me feel that all was right with the world again.
Same I remember WANTING this big 'who's laughing now?' moment for Team Rocket where they were allowed to upgrade and make the twerps take them seriously (don't we for all pitiful bad guys?) but never expected it to happen proper, and their personalities changing was very left field. Definitely played into BW seeming to have this more 'epic' feel at the start that something key had changed.
I was glad when they went into sort of the compromise era in late BW/early XY, being comical again but still forcing proper fights from the twerps instead of interchangeable one sided beatings, shame that didn't last though, would have made that change up remain a key moment in the show.
Seriously though, a lot of SM's trend breaking felt big though. Ash winning a league AND the exhibition match, mythicals going to his, Lillie, and Mallow's teams, Team Rocket fainting Ash's Pokemon, EVERYONE getting the main series gimmick, Misty, Brock and Jigglypuff returning, and just the overall unpredictability in storytelling. Not to mention how damn succinctly played nearly all of it was.
Melmetal vs Silvally felt like something that wouldn't have happened ever in earlier series, an 'Olympus mon' battle between two key characters. Really felt like the development cap had been raised a good deal by then.