"indie games still look indie"
This reminds me of that primal, societal fear that Winston tries to threaten O'Brien with in 1984: "Sooner or later they will see you for what you are, and then they will tear you to pieces." That feeling that the first ape who was cognizant that they were stealing from another ape felt, knowing that they were fundamentally lying and cheating someone else and they had to hide that or get torn to pieces.
I dearly wish that I could cite whoever planted this notion in my head, but what I'm getting at is that the "acceptance" of indie games feels like it's always been kind of correlated with how "non-indie" those indie games looked. Cave Story looked exactly like a SNES game. Super Meat Boy did unique things with vector-like shapes and giant, zoomed-out screens that hid its low pixel/texture fidelity. Minecraft did a similar thing by trading model and texture quality for scale. Alien Hominid, World of Goo and Braid were carried on their unique 2D artwork design that felt like it was designed that way, instead of "we aren't skilled enough/able to afford to do something else." I think that's the crux of it - that indie games were accepted only when they didn't give the impression that they only looked the way they did due to incompetence or lack of funds, but on PURPOSE.
You can see this by comparing the relative lack of success that engine-made games had in the 90s and early 2000s. 2D games made in RSD Game-Maker and Clickteam's products (and to a lesser extent, Game Maker 4-6) had this obvious jank in physics and gameplay that, even if they were sold, often didn't result in any noteworthy numbers. This lack of funds - or the incompetence of being unable to sprite or compose - often led them to use graphics and music from existing games, such as Sonic, Mario, and Mega Man. Even if you had the capability, or at least the willingness to learn to make your own, it was very hard to dig up the intrinsic motivation to do so when the underlying programming would still make your game feel crude and "indie-like" unless you had the programming chops behind your game that Cave Story did. Otherwise, consumers would "see you for what you were," knowing that they deserved better games to ask them to spend their time with. The same happened with interactive fiction's attempted resurrection in the 90s by Adventions and Cascade Mountain Publishing. Even though good engines such as TADS and Inform had finally come to make writing your own Infocom-quality - and beyond, in my opinion - interactive fiction, nobody wanted a "crude" graphicless, soundless game that was interacted with via typing. Although I disagree that this makes the genre invalid, that counted as "jank" for people. The general public felt that they deserved better and so these games sold in small numbers. I'll get to games "being as good as their forefathers but no one cared" later.
This funding model continued with the rise of compensated Flash games, where games, formerly given away for free (because again, why all that effort) around 2005, were usually not sold but rather given away with an ad-supported model as seen in the MochiAds model and with success in, for example, the Papa Louie games. Papa Louie didn't try to sell itself to you as an equal. It didn't even try. It just said "okay, you'll get a free game with addicting restaurant-management gameplay and in return you can watch these ads." It gave you the game before asking you to pay for it, unlike AAA games. It didn't even pretend that it could compete at that level (This type of shareware/time-trial was also seen in Apogee/ID's works in the 90s and casual games like Diner Dash in the aughts.)
As the Digital Antiquarian, Jimmy Maher, says on the commercial death of interactive fiction and point and click adventures, there seemed to be this sense among a lot of gamers that the current genres in the artform weren't valid in and of themselves, but merely as stopgaps until computers advanced enough to give you the "optimal version" of what the current games merely asked you to imagine you were playing.
Zork didn't have graphics, but it would have to do.
Wizardry and Ultima didn't have real-time gameplay, but it would have to do.
2D Sonic and Zelda didn't have 3D graphics, but it would have to do.
You can see that these games' sequels tried to reinvent themselves to the public later with all those things they "lacked," right? Return to Zork had graphics. Wizardry 8 and Ultimas 7-9 had real-time gameplay. Four years after Link's Awakening, Zelda was "finally" 3D, and the same goes for Sonic Adventure four years after Sonic & Knuckles.
I understand that I set up two seemingly-competing ideas - people being unable to program games, so they felt janky, and nobody wanted to pay for them, and then finally getting good engines that made games that felt just as good to play as the 80s/90s classics, but they still looked cheap, and nobody wanted to pay for them - but that's what I tried to set up earlier. That a lot of gamers seem to try to "sniff out" these games like a shark smelling blood and "see them for what they are" so that they don't get scammed - if you're incompetent and can't make an AAA game, they'll see you for what you are. If you can't afford to produce an AAA game, they'll see you for what you are.
I feel like a lot of the disparagement by the public and fear by the developers towards games "looking indie" is still rooted in that sentiment. That Zork, Ultima 4, Sonic 1, and Link to the Past weren't what consumers REALLY wanted, and that the companies were just selling them a stopgap. Now that fully 3D games have come about, selling a game that isn't - or God forbid, being proud of being so - still raises a certain type of forumgoer's hackles. "I'm tired of 2D stuff," they say. It feels like a conspiracy - a scam by indie developers - to them to suggest that 2D games are just as good as 3D games. They feel like 2D stuff is only borne from incompetence or a lack of funds, and that 3D stuff is the platonic ideal that the medium should converge towards.
And, in their defense, it can be kind of frustrating if you buy into what the publishers told you. Ocarina of Time was the "natural evolution" of Link to the Past, and Twilight Princess was the natural evolution on top of that game. Final Fantasy VII is the heir to FFVI, and so FFX is. Even Mario took a break from 2D games for about a decade. It feels like the misguided question "why are there still monkeys around?" as if evolving is the goal for every game. I'd also like to be charitable and point out that if you want something like Super Mario 64, or Ocarina of Time, or Final Fantasy VII... there still is kind of a paucity. Minecraft is the only 3D game that I've seen remotely "pulling a Cave Story," and not only did it get a second coder, but it eventually got its own musicians and artists. "Real" ones, not Notch and Jeb messing around, because now that Microsoft owns it, they don't want to be seen as being incompetent and scamming you into asking for a cheap-looking game.
I guess what I wanted to say is that, in their rush to sell new games, there is a concerted effort by big publishers to tell people that "You didn't really want Zork, Ultima, King's Quest, Sonic, or Zelda. We just couldn't give you what you really deserved, and we're sorry, but now we can! Go buy it!" that makes people think that interactive fiction, RPGs, adventure games, 2D platformers, and 2D action-adventure games are inherently primitive and unlikeable - that anyone who said they liked them way back when was just tricked into thinking they did because they didn't know better. (This extends to the graphics and sound of them, as well.) Sadly, this has killed off a lot of the genres of game I liked as a kid, even the 3D ones such as Petz and The Dog Island. You're either an F2P mobile title or an AAA title, and even that certain genres are only suitable for the former. The AAA companies have successfully tricked a lot of people into thinking that certain genres or even art styles "don't deserve" to be paid for because they are supposedly borne of incompetence or poverty. I wish adults could look at games with child-like eyes again, where they didn't mind that their imagination "filled in the blanks" for the laconic graphics and writing because what the game DID provide was legitimately enjoyable on its own merits.