When writing a new website I, like everyone else, like to take shortcuts.
This by itself is not a bad thing,
We stand on the shoulders of giants after all.
If you strip bootstrap down to just the basics, normalize and grid, you can get this down to under 15kb. This will reduce load times, improve your site's render time in older browsers (IE9) and make it easier to debug any rendering issues. For Bootstrap (My choice for a starter template) the easiest way to do this is to first copy out the variables.less file to your local directory, and the bootstrap.less file. Comment out all of the imports except for the for the required items and you're ready to get started:
From here you can add your own less files to the bottom to add-on and take precedent for any overrides to the basic bootstrap theme. As well as enable any portions of Bootstrap you wish to use on your site.