Because of the various changes in jQuery (for the betterment of all I might add) certain functions no longer work as you have experienced. jQuery Migrate is not only for fixing your deprecated scripts, it will also display the issues that have been found in the browser's console for the use of fixing the issues. I would suggest that you read up on it here and make the appropriate changes the the skin's scripts to future proof your skin, it will also mean that you won't have to include jQuery Migrate and your load time will be faster.
Sometimes updating things can be a pain, but with the internet always growing it's necessary.
Hope that helps,