This looks great, I just forked it and will have a play around with it within the next week. The biggest gripe I have with CSS frameworks like Bootstrap and Foundation is the amount of effort you need to go to in regards to how you write your markup and what classes you use, they are far too opinionated until you reach the point you spend more time undoing default CSS styles than you do writing your own. Bootstrap is a great example of this, you define a container, then you define a row and then you add in your grid classes and if you want to nest a grid item within a grid, you have to introduce another row element to do so, it can get messy.
My biggest gripe concerning Bootstrap is that it's listed as a project requirement, for whatever reason, and the designers refuse to design according to Bootstrap standards. For me that's been the main reason of having to tweak the defaults beyond their original intent. It can eventually reach a point where it's better to dump Bootstrap and build from scratch.
As for Bootstrap's grid system and nesting grids: I would think all grid systems work this way. I'm not sure how it would work otherwise. It's the same as nesting tables, you'll run into problems if you aren't careful and plan ahead. I would imagine in many ways that nested grid may not actually need to be a grid based on the purpose of Bootstrap's grid system. I bet a series of inline-block elements would serve the same purpose in many cases.
I had exactly the same frustration with Bootstrap and others. You need to spend a lot of time to learn them and in the end you end up with a lot of changes to their styles anyway. So, what's the point in having them in the first place? :) Anyway, I'd love to see your contribution, if interested.
The point is to use them for prototypes and then throw away, alas it is never done.
My personal opinion is that without CSS frameworks the web would be a better place. Not is is common just throw a bunch of frameworks (js and css) into the heap and call it a day.
As much as the one size fits all of bootstrap frustrates me, were you around before bootstrap?
Before-bootstrap is like before-jquery, you really can't understand the colossal contribution of either unless you were there. And just how much of a mess it was.
The dev world is unquestionably better for bootstrap.
Most cases of dislike towards things like Bootstrap is due to not understanding how to use it. It's a case of blaming the tool for not working the way it wasn't designed. Like, as an extreme example, screwdrivers really suck because they can't drive in nails very well.
I believe your first sentence illustrates my point.