we use an exploded web directory for our web module (Java EE Build Settings / Web Module Exploded Directory), but point the path directly to the local checkout of our web root. Hence we do not require the 'synchronize' feature that was present in previous releases.
However, we do not exclude the directory from the module content (checkbox 'exclude from module content'). Yet this checkbox is checked each time we reopen the project. This is rather annoying since the entire web cache will be rebuilt each time when you uncheck this option, which can take rather looooooong in large projects like ours ;)
Concerning the 'synchronize' feature I assume IDEA now intelligently decides on its own when to synchronize, meaning that in our case it will not.