Adobe Experience Manager is being used by the College of Agricultural and Environmental Sciences at the University of Georgia, a separate entity from the central IT system. We currently have over 100 websites on an older editing program that are being migrated to AEM. By the end of the migration, it will be used by about 80% of our college.
Upgrading and applying patches can be hit or miss - I recommend backups because of the potential to damage the existing infrastructure
Space management is an issue - every change or request takes up space that can be reclaimed, but only through a complicated procedure done through command prompts. There was no documentation for this on their site and we had to use a third party to create the procedure. It has to be run manually.
There isn't a good backup system, particularly one that can be scheduled to run reliably.
If you have a number of smaller parts of your organization that you want to maintain the same look & feel as the rest of the organization, it is easy to create a base site and then let them customize. Also, if you have contributors of content who are not involved in the web site maintenance - our professors, for example - they can enter the text on a basic page which is then incorporated through tagging.