Well, Mega Evolution for one thing. New battle styles, such as Triple, Rotation, Inverse and Battle Royal in later generations. HMs have been removed from the games completely since Generation 7. There's also now regional variants that are in Generation 7, but only of Kanto Pokemon. As for minor changes: you can now pass down Pokeballs and natures through breeding through various methods. Grass-type Pokemon can no longer be hit by Spore moves, Steel types are no longer resistant towards Dark and Ghost type moves, and there's been a new type introduced called the Fairy type, which is Immune to Dragon, weak to Steel, Poison and takes neutral damage to Bug, Fighting, and Dark. Oh, and some Pokemon have gotten base stat increases, which is pretty minor, at best. The Experience Share has also been made a Key Item, instead of a Hold Item, as of Pokemon X/Y. Wild Pokemon also give EXP after you've caught them as well, starting with X/Y.
That's all I can think of, though.