d20 itself was an innovation. No it's not the first of it's kind of thing - even if people here might think it is, but the way it was done, and what it done with make it a major innovation in RPGs.
The new Marvel RPG is a solid innovation as a completely non random RPG that at the same time has a mechanics based approach with objective resolution that is not predetermined but is based on strategy and tactics. In truth, at present it is the only RPG -EVER- that has taken a tactics based approach as it's system of resolution (even previous non random RPGs failed to truly deliver this). I'm not yet sure if I like or dislike the game, but I've seen enough to know it's full of major innovations.
7th Sea had an innovation I've yet to see resurface, but if it does it could completely rewrite one popular aspect of nearly all non D20 based RPGs... In 7th Sea disads/flaws cost points rather than reward them, but give XP when they come up in play. Thsi completely flips the axiom of disads from something the players try to trick the GM into avoiding into something the players strive to have actively hinder their characters. Couple that with a good list of disads and you could go a long way towards encouraging roleplay and actually getting people to enjoy roleplay who were not previously inclined to it.
But now I'm going back in time, if I keep this up I'll end up on a discussion of Dice pools and generic RPGs... Let's move forward...
Sovereign Stone has a major innovation in it's magic system, which is a completely different way doing spells in d20 that allows for a much more open ended approach and a much more mystical result. It still needs work, but it shows amazing promise as a new angle.
Mutants and Masterminds had two major innovations for d20:
1: d20 without classes or levels. The point based design system works and could be adopted into other genres by wise parties.
2: d20 without hitpoints. The damage save completely revolutionizes tracking injury in an RPG and moves it from 'bean counting' where a player knows just how much injury they can take and how long they can keep fighting to something where they never know just when they will fail and fall, so they handle risk taking in a much more -in the moment- manner. You feel the danger much more in MnM, because you cannot predict the results ahead of time.
There are many more innovations out there... but those are the ones I know best. For people not willing to go as far as Sovereign Stone's magic system, the system presented in AEG's Magic is a minor innovation. But it's actually just a reflection of a common first edition house rule brought into d20.