Several things changed since last time this post was active.
I. First of all, geolocation works with Ionic (it was never under question). Cordova.js file was also never a problem. If you want to get a correct location just wrap you code into device ready event.
II.Use ngCordova Geolocation plugin
III.If you’re using Cordova 4.0 + version make sure to install Cordova Whitelist plugin, Google Maps will not work with it.
IV. Whitelist plugin comes with new HTML5 meta tag, you MUST include it if you want maps to work. Default meta tag (found in official plugin github link) will not work with Google Maps, use this one instead:
<meta http-equiv="Content-Security-Policy" content="default-src *; script-src 'self' 'unsafe-inline' 'unsafe-eval' *; style-src 'self' 'unsafe-inline' *">
Everything said here including working example can be found here: Using Cordova Geoloacation API with Google Maps in Ionic Framework