Compare instance level information
Like configuration settings, security info (logins, server roles...), linked servers, jobs, SSIS catalog info for SQL2012 (folders, environments, security, projects, packages...) etc.
Please note that some instance level objects are more important (Login, Linked Server, …) because they used in procedures and functions.
There are now free competitors like Aireforge that do a better job of SQL server configuration and database comparison than SQL Compare. We are a Redgate customer and I have been asking your support for this feature for years.
Might want to take a look at https://dbatools.io/
David Potter commented
I have found that the in ability for the app to compare Jobs, is a big gap. When migrating servers.. the ability to handle configuration settings, security info, ect would also be a big help.