Add the ability to lock down file write access per application (so one a compromised application cannot affect other)
Applications on the same server currently have write access to each others' files by default, which is an unnecessary security risk. For example, if you have multiple Wordpress applications on the same server and one gets compromised, the hacker could also compromise any other applications on the same server. If possible, it would be worthwhile to at least have the option to lock down file write access on a per application basis. I believe you already have apache running under separate users for each application, so this might be as simple as disabling the www-data group permissions.