It comes down to the same issues that I have with templates of tumblr,posterous and wp. They all look the same. I think bootstrap should be used as a way to jumpstart the design process and not built a WHOLE website using the components bootstrap provides.
When I see that grey-black gradient nav bar i go "Haizz yet another bootstrap site."
I love the look of bootstrap sites. Having identical looking sites beats the shitty design most of these sites would have had before bootstrap.