1) By going mobile first, browsers such as IE8 which don't implement media queries now require you to add in an extra 15KB of CSS to fix it ( https://code.google.com/p/css3-mediaqueries-js/ ) , whereas all smart phones support media queries already.
2) By having glyphicons as fonts rather than sprites, we gain the ability to precisely size, place and colour the icon, but have now broken accessibility as the vision impaired or those choosing to have their browser use user specified fonts now get random characters displayed.
And that is it... the only 2 issues from a site currently in production and with users.
I should note that there are some really good bits, the extra support for mixins for example. I also personally also love that the new grid is now fluid and responsive by default. I like the declarative nature of col-lg-* and col-sm-* (though think a col-md-* should exist for fine-tuning layout tablets).
The biggest hurdle in coming from 2 to 3 is really the grid changes, the move to fluid, the changing of the class names. There are some minor changes to class names for buttons, forms, text colours, etc... but nothing that requires too much thought to deal with when upgrading.
2) Icon Fonts should make use of the Unicode Private Use Areas[2]. Screen readers should not attempt to make sense of these code points, and you can add title tags to enhance accessibility.
[1] https://github.com/scottjehl/Respond [2] https://en.wikipedia.org/wiki/Private_Use_%28Unicode%29
On #2, that might fix screenreaders but it still looks ugly if a user chooses their own font: https://f.cloud.github.com/assets/1126981/506313/554bfab4-bd...
What we're likely to do is to create SVG icons and use those. with .png fallback... much like how Zurb are doing so: http://zurb.com/playground/social-webicons
Refactor components to be more mixin-friendly.
Honestly, Bootstrap will really benefit from being easier to fit into your own markup, rather than forcing your markup to fit Bootstrap. I mean: that's what CSS is kinda all about.
Bootstrap was so painful the moment you deviate from their styles. Similar to Rails when deviating from the "rails way".
"Instead of .span and .offset, we're now using .col-span- and .col-offset-."
I can blaze through views using .row & .span in HAML, not so much now. I envision tons of personal errors in the short term as I transition projects to BS3.
===========
Issue #2, does anyone know why Glyphicons won out over Font Awesome? ( http://fortawesome.github.io/Font-Awesome/ ) Isn't Glyphicons only free in .png? I'm kinda confused about how the licensing works here: http://glyphicons.com/
===========
Issue #3 [This is under the modal section...] This sounds like a bad idea, I personally don't have an ios3/4 device handy, but someone should be on that for something as big as bootstrap:
"Test on iOS5. Not sure if we need to go older, but I want to check here to see how well fixed is supported."
From Bootstrap docs (http://twitter.github.io/bootstrap/base-css.html#icons):
"Glyphicons Halflings are normally not available for free, but an arrangement between Bootstrap and the Glyphicons creators have made this possible at no cost to you as developers. As a thank you, we ask you to include an optional link back to Glyphicons whenever practical."
Seriously, how is that in any way helpful?
[1]: https://github.com/FortAwesome/Font-Awesome/blob/master/buil...