The more people stop using Bootstrap as a complete design the happier I will be.
Bootstrap is definitely useful if you're just tinkering - it makes a minimum viable product look sort of legit ;)
But I would certainly invest in specialized developers to make a lighter-weight, in-house UI if I were really serious about a website.
What is always good to have is a designer or at least a developer with an eye for aesthetics, to use the Bootstrap elements in an elegant way. Otherwise, what would you "hack" about HTML/CSS? Either reimplementing Bootstrap, or playing with the latest and greatest that won't work in anything else but the latest Chrome (see the IE6/7 discussion).
When used to build something that should be visibly unique, the visual design and appeal is something that should be created aside from bootstrap, maybe with the grid in mind, and delivered as mockups or pattern guides.
I suppose you could say it comes with a theme, but anyone who cares enough to complain about the theme should also be motivated enough to customize it.
A lot of web applications -- line-of-business but also consumer-oriented -- should NOT be visibly unique, and styling your own buttons not only is a big waste of time, but also reduces usability. Look at the WinForms/Cocoa/GTK environments to see the value of a single visual language in action (including their respective UI guides that help with a consistent experience). The popularity of Bootstrap tells you the need is still there -- for both the millions of developers who need to get the job done without reinventing too many wheels on top of broken hypertext, and for the users who appreciate not having to figure out a UI for the millionth time (just ask your boss/customer what they think of your boring Bootstrap app, they probably love it).