some responses to (some of) your points (btw, my numbering doesn't match yours):
1. Bootstrap in Core: I think in general Moodle should be moving away from this idea and putting everything front-end-ish in Themes where it can be examined and changed. Much like putting the front end code in renderers allows things to evolve, putting stuff into Themes lets people tweak things for their circumstances. When the next big thing comes along (even if it's only Bootstrap v3), it would be better if people could experiment with that, without having to work around hard-coded things in core. There already seems to be some move to this e.g. the filepicker images are in Base, the core CSS is in Base. If you don't inherit from Base you need to copy all that stuff across to your new theme, which is a relatively easy thing to do and makes it very easy to delete or change the bits you don't like.
2. Bootstrap in Core, part 2: I think it would be a very good idea if Moodle adopted the Bootstrap HTML conventions and rewrote the core renderers to output it. For example, if you want to add a pager go and look at Bootstrap's, if you want to add a form element go and look at Bootstrap's and copy the HTML. There's already talk about adopting standard conventions, it would be much better to use theirs than invent our own. This may seem to contradict the previous item but it's a thousand times easier to build a custom theme on Bootstrap's HTML than on what we've currently got. Note: I'm already experimenting with re-writing the renderers here: https://github.com/ds125v/moodle-theme_bootstrap_renderers and it works quite well. It also gives guidance on the ideal granularity of renderers (e.g. one for navbars, one for unstyled lists) that could then be easily be swapped for ones written to match Zurb or any other Bootstrap-alikes or rivals.
3. Grids are a surprisingly small part of moodle, it's basically one layout file. I originally did a grid with YUI when I was experimenting with an HTML5-based theme for Moodle and then redid it with Bootstrap. I don't recall any massive difference. Basically it comes down to which CSS files are you already including and what do you already have experience with. YUI was the first framework I remember doing grids, but they're ten-a-penny now. Like #1, put the decision in the Theme. (edit: regarding your accessability point, I don't recall either offering an easy way to put the content first in the HTML, I made myself feel better about it by using newer HTML5 tags and putting the main content in article tags and the blocks in aside tags, as well as header and footer.)
4. Resets: Bootstrap used to have its own reset but for version 2 they adopted a 3rd party project called normalize that takes a slightly different (and better) approach (see http://necolas.github.com/normalize.css/). YUI's Reset and Base styles are not only old-fashioned in that sense they also (and I literally couldn't believe they'd done this) add a horrid black 1px border round all table cells, working around which has caused weird bugs in Moodle (see https://tracker.moodle.org/browse/MDL-27774). This has, perhaps unfairly, turned me against YUI's reset more than the rational arguments at that github link. (Though #1 again, put the decision in the Theme, I believe there's already a bug open about this)
6. Class names collisions: I've went into more detail in the related bug, but basically the Moodle classnames are semi-random, full of historical leftovers and often unnecessary if you a) organise the HTML well and b) only target modern browsers (IE8+), whereas the Bootstrap classes are clean, modern and well organised. I think the Bootstrap one's win, even when it's a bit of a pain to change the current Moodle ones. Again, even if you wanted to do something totally un-bootstrappy you'd rather start with their classes and HTML than what's there currently.