"used to be." As if the indie core is for some reason immune to progress in price model just as much as it has been for years in gameplay and story development? I have zero interest in The Witness but considering Blow is a big reason there's a viable and sustainable indie field at all, and that he's been working on this game SINCE Braid helped kickstart indies into the forefront, why should I complain that his game is $40? It's got a budget comparable to the new Ratchet & Clank game, which is also $40. Being "indie" nowadays is essentially referring to a lack of a publisher, not the people developing it. If Blow put up his own money even before Sony swooped in and yanked exclusivity, and that investment needs to get paid back, he has all the right to competitively price his game.
Going to your example game, your key phrase "It looks amazing for this price" sort of breaks down why you're being entitled here - as if indie games don't deserve to have the graphical fidelity or pricing model of any other game. That line of thinking is almost as bad as when the world put down gaming as a kid's toy, because it was newer and more unfamiliar than movies or television. If this team physically can't - due to lack of resources - or doesn't want to make a game with better graphics that's a choice, a limitation, and the price reflects the need to recoup a lower budget. It says nothing of the honor or whatever you're trying to project onto this team that they designed a cheaper-budget game.
You should check out my YouTube channel, The Golden Bolt! I review all types of video games, both classic and modern, and I also give short flyover reviews of the free games each month on PlayStation Plus to tell you if they're worth downloading. After all, the games may be free, but your time is valuable!