I had similar concerns when I first started noticing bootstrap used on random websites I encountered. However, I think bootstrap will probably help increase the lower bound quality of sites while designers pushing the envelope will continue to do so, without or without bootstrap as a starting point.
I hope it WILL create a more homogenized web. Seriously, how many different kinds of push buttons do we need. The design creativity can better be applied elsewhere.
It kind of happened with Wordpress and Drupal default themes but the web is too big to go really that way and technology evolves very quickly, so today it's Twooter Bootstrap but tomorrow it will be NewFadCorp Boostrap.
I understand that you can re-skin but I'm thinking many folks will go with the pre-built look/feel.
Even so, this is awesome for getting stuff out quickly. Great job.