If icon size is an issue, you can try using Font Awesome: http://fortawesome.github.com/Font-Awesome/. It uses a font-face for the icons rather than sprites, so you can configure further in css by adjusting size and color, whereas bootstrap's icons are limited to black/white (plus some opacity). A potential gotcha with this approach is you need to be sure you can configure your web server to send the right content-type for the font files you'll send. I had to do some minor nginx configuration to get it right for certain browsers.
There are also pre-customized resources like bootswatch (http://bootswatch.com/) if you want to get a look at some of the possibilities.
And if you clone the bootstrap repo, you can fiddle around with the base LESS stylesheets to make quick changes that affect the full system (lots of stuff in variables.less: https://github.com/twitter/bootstrap/blob/master/less/variab...) of course.
I don't think the issues you listed are particularly significant unless you know that customization is going to be too costly in terms of time.