Indie does not mean low quality. It's just that there are a lot of low quality indie games. Many indie games that receive praise are praised for their mechanics or overall originality in story or otherwise, not because they necessarily push boundaries or offer revolutionary experiences. Fez, for example, is definitely fun for its perspective switching puzzling. Hotline Miami is fun for the fact that it's kind of a retro throwback that depends on reaction time and gamer ability. The rest of those, well, honestly, I haven't played them.
Admittedly, the vast majority of indie titles feel like flash games. Honestly, I think many indie games were intended to be flash games, but the developer saw a way to make a few bucks off of it and decided to limit exposure for the sake of the $10 they may make. The good ones tend to be the ones that act as exceptions though, feeling like full experiences in their own right even if they aren't necessarily the highest quality or most original works out there. Of course, then you have the best exceptions like Bastion that are just so ridiculously good you can't even compare them to the average indie title.