You won't get rid of Bootstrap. We use its classes and HTML structure. If you remap your own CSS to the same classes sure, but at that point you're just customizing Bootstrap which the below tools can significantly help you with.
bootstrap-live-customizer.com/
bootswatchr.com/
The other templates were removed, because they were no longer compatible and didn't have the time to rewrite all of the templates. Instead we'll eventually have a plugin that just lets you generate your own CB template with whatever colors you want (I've moved this project up on my TODO list).
The major complaints regarding Bootstrap are as follows.
1. Lack of semantics
A. I agree, but how do you use semantics in a generic framework? We've addressed this by adding our own semantic classes to elements. We try to always do this. In addition to that Bootstrap provides you with LESS and SASS. There's nothing stopping you from remapping that CSS to your own semantic classes.
2. Conflicting and bloated JS
A. Completely agree with this and is why we don't use its JS.
3. Every site looks the same!
A. I agree, but it's not Bootstrap at fault. It's lazy developers. Bootstrap can be VERY extensively customized with as little work as modifying the variable file, but the best approach is role your own theme (see the theme included with Bootstrap as an example).
4. Size
A. File size is a bit heavy, but with todays internet? Not a problem IMO.
Personally am looking forward to B4 and upgrading CB for it.