Disclaimer: Rosters don't count as innovative. Nor does a minor engine update. An overhaul is innovation and so is a completely new gaming experience altogether.
Indie games have hit the market hard by picking up where major developers/publishers like Activision with their Call of Duty series and EA with their sports brands have constantly lacked the time to innovate the market. Where has the actual innovation come from? Studios with bigger risks but also smaller in size. Indies. Indies are picking up where the big behemoth has forgotten its place. Why innovate when people buy the same thing over and over again? That's how big companies compare to small ones that struggle for cash and are lucky at times to make enough to survive.
I would say that major AAA publishers are bad for not taking risks but it just means they're too comfortable. I understand there's some publishers who take risk such as games like Sleeping Dogs and Dishonored proving that there exists a market for innovative new games. No one likes to have the same experience multiple times unless you play a series that hasn't tried hard enough to innovate whilst perpetuating that we need more.
Now if we compare AAAs to a smaller studio like Wolfire Games who i'm biased to say I love. They're a studio who has been helping other smaller studios like themselves get recognition for their games easier by their Humble Bundles. David Rosen and his team has proven that they can make unique games with specific engines for their titles and take all the development time to make it well worth playing. Receiver is a gun game where once you're dead then you're dead. Lagaru and its soon to be sequel proves that animal combat is awesome while having a deep and interesting story to make us love some of their characters.
What did Rosen innovate? Trying to be different with his studios games by making their own engines like for Overgrowth which while it may still be in the Alpha stages is proving to have a better engine than most AAA games and Receiver which shows that people care about realism in gun games other than simply pressing the reload button and dealing with recoil. He is one of the many example of unique innovation in the indie game industry. Mojang has proven that you don't need a story to sell a game, just the experience. The same could be said for Dear Esther. It's that you don't need extreme HD graphics to make a game sell. You also need that experience.
If we were to compare a vast majority of bajillion dollar development releases to a smaller Indie who has spent sweat and tears on their game while a bigger studio spends the work force of over 200-300 making the game as streamlined as possible without much regard for the experience. Who innovates the most? The bigger or smaller studio? Is a smaller studio release more emotional due to it being developed by a less than 100 team? Are big teams really necessary to make a game get complete within a 2-4 year deadline? You tell me. We're all gamers but i'm only ever just one.