Indie games have the same problem every form of media is running into: When there are no gatekeepers, and anyone can make media, how does one notice the good stuff while ignoring the crap.
To start off, let's accept that most of the stuff (in any medium) is crap. Making art is hard, and most people fail to execute on their vision, or they had a bad vision in the first place. As Theodore Sturgeon said, "90% of everything is crap."
So, given that, we are tasked with finding the 10% that isn't crap, but it's floating in a sea fo crap, so that's a difficult proposition. iTunes, which has this problem in spades, has tried both curation (recommended sections) and crowd-based evaluation (ratings and top lists) and is still a sea of crap studded with the occasional gem.
Steam, being more heavily curated, does a better job, but is still swamped with crap. PSN and XBLA, which are entirely curated, do a better job, too.
And then you come to stuff like XBLIG, which has no curation, but worse yet, has terrible tools for crowd-based rating and searching highly-evaluated games.
The issue isn't that no one loves indie games, the issue is that no one knows whether they love a particular indie game or not, because it's incredibly hard to tell if a game is any good with research that most people are unwilling to do. GAF and places like it have a role in this, acting as external crowd-based rating systems, as do media outlets like Polygon/Escapist/etc.
So far, no one seems to have figured out a great way to do it. I can't think of any self-publishing concern that doesn't have this problem, from Amazon's Kindle library to the various sites that have tried this with film.
The only thing we do know is that the real gems, the stunners, tend to rise to the top on word of mouth. Short films go viral, self-published books explode via word of mouth, and indie games wind up plastered all over forums and media sites.
The problem isn't the very top-tier of indie games getting ignored, it's the midlist. The games that are good, but not quite spectacular enough to start a massive word of mouth campaign like FTL. A studio game can be midlist and still find its audience because studios can market it heavily, but without a marketing budget, the midlist indie games become invisible. They don't show up on the top rated pages, no one's hyping them in the forums, etc. That's the real loss, because some of them are gems, albeit rough gems.
I don't have the answer to this, anymore than anyone else does, but this is the issue. Attention is the new currency in media. If you can get the attention, the money will follow, but getting the attention gets harder every time a new concern opens up an easy route to making games, and more and more indies flood the market.
