You've only just now noticed this?
I hate to say it, but it's been like this since Braid and Limbo hit the scene in the first place.
But hey, don't worry, just like in the AAA space, there are still tons of games that are trying to push the mold, like Aarklash Legacy, Bastion, The Banner Saga, Cloudbuilt, Darkest Dungeon, Dex, Divinity: Original Sin, Eldritch, Endless Legend, Grim Dawn, Hard Reset, Invisible, Inc., Legend of Grimrock 2, Sanctum 2, Satellite Reign, Shadowrun Returns/Dragonfall/Hong Kong, Starpoint Gemini 2, Superhot, Transistor, Undertale, and Ziggurat.
EDIT: The relative "indieness" of some of those could be debated if you believe that in order to be "truly indie" a developer can't go through a publisher at all, but, well. I think they still count.