I prefer to keep functions in plugins, so that your site will keep working when you change themes, but I understand where the developers who want a leaner site with less script redundancy are coming from when they prefer to build in just the functions they need.

Fine if you're never going to change themes or can somehow foresee all the functions you'll ever need or will still be around to do all your own updating as WP adds new things like widgets, tags, and post thumbnails. Not so good otherwise. (And for those of us who aren't developers and don't plan to be, not really an option.)

Themes with theme options--which means, in essence, built-in plugins--are handy for the people with no knowledge of the way WP works, but problematic for people who have been with WP since the early days. (I wrote about this after my first encounters with themes like this, which were hair-tearing experiences.)