In Bootstrap 2.x.x Glyphyicons were in image format, hence you can't increase the size, change the color, background-color, etc easily. However, font-awesome gives you scalable vector icons that can instantly be customized — size, color, drop-shadow, and anything that can be done with the power of CSS.
Font-awesome is really an alternative for Glyphyicons which is getting updated time-to-time with new icons. Fat and Mdo are planning to integrate Font-awesome in bootstrap version 3 as a replacement for Glyphyicons.
My suggestion is you use bootstrap with font-awesome. First include bootstrap css and then Font-awesome css, so that the Glyphyicons will be override by font-awesome.
UPDATE
In bootstrap version 3.x.x glyphicons become font format, which will render nicely even in 12px font-size. If you're using the latest version of fontawesome, i.e. 4.01, you can use both glyphicons with fontawesome.