@pdewouters– You can definitely include Piklist as a library. Just include the main piklist.php in your functions.php file.
1) You will need to keep up to date on Piklist upgrades, and upgrade your theme accordingly.
2) The user will get an error if they install your theme AND the Piklist plugin. The next version of Piklist will include a check for this.
3) We want Piklist to be the FIRST PLUGIN a user installs… so that is our primary goal. This way they can take advantage of your theme, and a bunch of awesome plugins we plan to release., like WordPress Helpers.