I agree that having bootstrap as a common standard is doing more good than harm. However bootstrap is tied much more to design esthetics than interfaces.
With that being said, website designs have defiantly shown trends over the years (as have operating system "themes"). So I think we'll see something else come along to replace the bootstrap eventually according to the "standards" of the next greatest design phase.
Note Bootstrap does make a solid case for using standard components such as LESS, CSS and jQuery.
Are you a web designer? Because some folks (yours truly included) don't have great design sense, so putting up a bootstrap site is much better than the alternative 2003 geo-cities look that is just as easy to create. When it comes to the lesser of two evils, i'd choose "less" and bootstrap.
I agree. I think you can use bootstrap as a starting point then move on from there. It just helps things look nice while you allocate resources elsewhere for the time being.