This is the key to Bootstrap (or similar css frameworks). It's not intended to be a theme. If you want to just have the css/html ready for you to do some documentation or a project that has no need for any visual differentiation, then go ahead and use vanilla.
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.
Come on yes it is (was) intended to be a theme , that's why it is so successfull. Grid frameworks existed well before bootstrap , and most developers did not use them.
Grid frameworks like 960gs never became as popular as Bootstrap because Boostrap is as much about formatting content (including forms and UI elements) as it is about the responsive grid layout.
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.
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.