Ember is actually composed of many smaller, independent packages. For example, we built four microlibraries for use in Ember that you can use totally independently: router.js, route-recognizer.js, rsvp.js and metamorph.js.
Additionally, many people use other great projects from the JavaScript ecosystem to do Ember development, like D3, Crossfilter, mocha, Jasmine, etc. Your assertion that it does not work together or integrate with other tools is 100% false.