Unless you're targeting developers or Silicon Valley who cares? Most people couldn't tell you the difference between a Bootstrap site or a non-bootstrap site, even if they could its unlikely they would actually care. As a dev who admittedly sucks at CSS I'll take better looking and clone-like (and cross-browser) over ugly and unique any day.
Also, check out oss/bootstrap/docs/download.html#variables a new feature in the docs that makes customizing really easy even for someone who doesn't know CSS!
It just looks like you chimed in to show the negative side, but didn't even check out the new code.
Thank you to anyone who worked on the project, 2.0 is awesome. Responsive design is nailed down, adding and removing components is even easier than before and the docs are awesome. Good stuff here.