Aside from the Google issue, I think honestly the biggest thing is that MS was still charging OEMs a licensing fee where Android wasn't. They eventually let go of the fee, but it was too late. I think that killed WP more than anything.
From what I remember, no. I think play services is a separate license which is also free, as long as you sign something called the Open Handset Agreement (or something like that), which basically forces OEMs to follow a bunch of rules about pre-installed/default apps and home screen placement, etc.
The one example I remember being mentioned at some point is that the google search bar widget must be on the first home page of any phone sold by OEMs (of course users are free to change that if they wish). Other little things like that. Instead of making money from licenses, Google makes money by nudging users into its ad-revenue generating services.
Google doesn't collect a paid license fee for Google Apps on Android, but they have fairly significant nonmonetary agreements, essentially barring the OEMs from using Google's competitors, making Google's products the default, dictating where Google Apps must be placed on the home screen, etc.
Some of the larger OEMs might be able to negotiate revenue sharing agreements from Play purchases, but inside the Google Apps is definitely where Google makes its money, on app sales and ad targeting based on data collected by Google hoovering up everyone's mobile data and location.
