I'm not really sure if there have been many innovations in RPGs in recent games. The recent ones I can think of are collaborative games where the GM is more of a guide than a dictator, and the integration with digitial (edit: And using funny dice which is all the craze now).
Going back in time I remember when Storyteller/White Wolf arrived and that shook up the RPG scene with their emphasis on building a system that flowed smoothly at the cost of mechanical detail, and when we went level-less and class-less with games like Runequest. This list is of course in no way correct or complete nor do I intend it to be. Just things I noticed over time.
What I find amazing is that RPGs could have been invented in ancient times (papyrus sheets and bone dice) but no-one thought of it until the 1970s. Sometimes I wonder if there's something truly amazing, and simple, but no-one had the idea yet.