Jquery version issues: Flexslider doesn't works only with 1.5 and bootstrap needs 1.8+
I recommend the jQuery Multi module.

It allows you to use the default drupal jQuery version for most of you site, and use newer versions of jQuery just for plugins that require it.

It gives an administration page where you can choose which libraries to load using the newer jQuery.

It also has hooks you can use to tell it to load your libraries using different jQuery versions.

If you are writing custom js it also namespaces the jquery versions so you can do something like:

(function ($) {
  // All your code here
})(jq172);


That is how the module would namespace jQuery 1.7.2 and you can load your scripts like that to use the newer versions.

One thing to note is that if your plugins with new jQuery require things like jquery UI, jquery.once etc., that drupal core uses already, you have to make sure they are added a second time, so they are added to the normal drupal jquery and the newer one.