One of the main reasons my company went to a dedicated ticketing system like service desk was to centrally manage our IT issues in a efficient and organized manner. For the most part ServiceDesk has done this.
An issue I've run into is the option to "Show in Portal" for end users (customers). By default when a user creates/submits there own ticket via e-mail or portal, "Show in Portal" is checked by default. When a User (technician) creates a ticket this option is turn off by default.
From what Ive seen there is no way to set this by default. The issue we run into is small but has a big impact on certain customers we just so happen to forget to check this option.