We use Zendesk in multiple departments at this company. We use it as a customer relationship management tool mainly for its chat and email to ticket capabilities to enhance our customer support processes. We also utilize its Communities and Help Center.
Limited functionality - Compared to some of the competitors out there, Zendesk has a long way to go, offering limited functionality such as advanced trigger logic, the limited use of the CC field, and the lack of integration between their chat and ticket reporting.
Analytics - Reporting is only based off of ticket fields and hardly anything else. This makes it hard to really track agent productivity and more importantly, it is hard to integrate into your business intelligent systems.
Roles and Permissions - Creating roles and permissions is very limited. I would like to have more control over what users can and cannot see within the user interface as well as access to functionality.
Positive - We can track emails and similar threads all on 1 ticket, which is increased our productivity and efficiency.
Negative - Due to limitations of the CC field, it has become a huge learning curve to use this new system in replacement of email support, costing us additional training resources.
Negative - Because analytics makes it hard for our Business Intelligent unit to integrate into their system, it has become a lot of manual work, and this costs us more resources to support his manual process.
Positive - Chat support efficiency and SLAs have improved due to the ease of chat transcripts, client history access, and transferring capabilities, saving us money on client support.
Zendesk is well suited for smaller support groups or companies. They can definitely leverage the efficiency gained by the business automations, macros, and custom integrations that Zendesk is great at providing.
Due to the customizing limitations of permissions/roles, and the lesser flexibility of this system compared to some of the major players such as Salesforce, it's harder to implement for a larger organization that needs very specific configuration and individualization for their use-case/department.
Lastly, analytics isn't a strong point, and this is crucial to the success of your business when looking at ROI for utilizing this system.