Alright, so here is the update and the current strategy I am using going forward:
Windows 8 games: Use the windows 8 advertising plugin to display the ads in layouts and position them just like, you would a sprite. If the user purchases the game set a global variable that tracks if the game was purchased and disables the ads. This is currently working fine in my apps.
Windows Phone: Wait for thehen updated Windows Phone 8 plugin to add advertising support.
All other platforms(Android/iOS): CocoonJS ad support via Admob/Mopub. Use the cocoonJS object (Until a better solution via crosswalk is implemented). Implement logic to check if the app has been purchased (or an IAP "App" has been purchased) and if so disable the ads.
Hoping this will work on Android, iOS, Amazon(Kindle), Nook.
Unless anyone has any better suggestions...