I find these criticisms regarding the ability to recognize a "Twitter Bootstrap site" to be inconsiderate of the audience for which the sites were really created.
Generally speaking, the startup development community exposes themselves to new websites on a pretty frequent basis. Just because we can recognize a particular CSS framework, doesn't mean the intended audience of the website can.
I would be surprised if it wasn't an extremely small percentage of website users that would be able to recognize "just another Twitter Bootstrap site."
Don't let yourself get caught up in the bubble of the ever-critical development community. If you're building a site just to please folks within that community, you should probably do a bit more research on who you really want your target demographic to be.