When deciding between Jira Cloud and Jira Server, it is important to consider the amount of time required for system administration since maintaining server infrastructure can be resource-intensive. The commercial apps you would like to use are also crucial since not all apps are available or work in the same way on both platforms. Finally, the ability to integrate with an external user directory, such as a company LDAP directory, is essential for many organizations relying on centralized user management. Therefore, the three key factors to consider are system administration time, commercial apps compatibility, and external user directory integration.