Honestly, from what I hear in the indie stuff, there seems to be a determined effort to be "low-fi" as opposed to "polished", and "untrained" as opposed to "well-trained" or the idea of "excelling at one's instrument". And in a lot of cases, it seems to be a matter of posturing and image rather than reality, because there are some pretty talented people out there doing lower quality music than they're capable of. I think of Sufjan Stevens or Akron/Family (two indie darlings that I actually enjoy listening to, but wish they'd work just a little harder at their craft).
I think it may be interesting to see how some of these artists mature in the next few years. Meanwhile, I think they need to get over their attitude of being so reactionary against "overproduction", and actually produce better crafted and better sounding records.