The majority of my personal skepticism toward independent games is the overwhelming disregard for a solid gameplay experience in favor of making one's game into some kind of art project. I was looking forward to this upsurge of independent development being a departure from cheap thrills and attempts to impress us with the superficial rather than just making a good freaking game that can stand the test of time, but most independent games, made by people who experienced an era of simplicity and examples of how much you can do with so little are among the most superficial of all, seemingly completely missing the point of what good games teach us, or worse, not caring in the first place in an effort to shove how pretentious and full of themselves they can be in our faces.
I'm also getting fed up of the "retro" hook that ends up consistently being an excuse to shovel the above while also making it look and sound like shit, because that's just how the developer thought things looked back then. Many of the things that endeared people to many games of the past - engaging gameplay, testing the player's knowledge of what they were capable of, scaling difficulty, memorable compositions, making the most of the technology available, and so forth - seem to be lost on the very people who experienced the era, and the results are often unsavory to people who appreciate more than "Look, I made a video game that looks kind of like the games you used to play, but it's dark and brooding and shit!"
On that note, I'm sorry, while it's neat you made a game and got someone to publish it and everything, and you spent more than half an hour writing the story, that in and of itself simply doesn't impress me; there's got to be some meat in there too, something I should be able to judge on level with anything else, not "for an independent game". And before you say "these games can't possibly compete with big budget block busters!", most big budget block busters are garbage, and those that aren't aren't so because of the money behind them. Incidentally, most independent games are garbage, and those that aren't aren't so because they're independent, so as it turns out, they can compete fine on equal footing. Of course, I'm willing to admit I may have different standards than most; I never asked for cinematic cutscenes are gritty realism in video games, and those aren't the things that win me over when a game featuring them turns out to be something other than garbage.
Regardless of my tastes, the question developers should ask themselves, independent or otherwise, is "Is the player going to want to play this thing again when they're done? Is there anything to bring them back?", and the answer is usually "No, there isn't". The gameplay is not a vehicle for the plot, or the setting, or any such things; the gameplay is in the driver's seat, and everything else is in the back seat and maybe picks a radio station now and again, and if your first priority is "a moving tale" when developing your video game, you're doing it wrong, period. If you insist on making plot a focus, it should either be "an exciting experience, featuring a moving tale" or "the player is the driving force of my moving tale". Not "the player character". The player. They and the gameplay should be the catalyst for the development of the experience, and a few floating platforms and switch puzzles between bits of broody dialogue don't cut it, sorry.
I don't get off on raining on peoples' parade - I want these games to be largely great because they have the ability to take video games away from the spectacle they've become, to make us learn and grow throughout the course of an experience, to be challenged by adversity and come out on top with our own hands. That's what I truly love about video games, and I feel the player is being taken out of the experience more and more as time passes, being robbed of those challenges and those triumphs, that exhilarating feeling of "Yes, I did it!", or "God, I was awesome just now." Video games are becoming cold and lifeless to me, and the people who should understand what makes them unique, makes them special as a media are just largely contributing to the problem. Granted, that may just be my problem, but I still think we'd all be better off if the focus on making the player the center of the experience returned, rather than just the thing scrolling the text or moving to the next cutscene. I'm not even saying the flashy lights and plot focus need to go altogether; I'd just like to be enjoying myself in the meantime.