One of my favorite developments by VMware is the vCenter Server Virtual Appliance (vCSA) as I want to get rid of as much Windows Machines as possible in my environments. It also simplifies the administration because you do not to have to configure and patch another operating system. Unfortunately the vCSA is really rare in a production environment. In my opinion this is caused by the fact that the vCenter Server Appliance always has some limitations, which are often not completely understood.
Here are the limitations from the current version of VMware vCenter Server Appliance 5.1:
The embedded Database only supports up to 5 hosts and 50 virtual machines. This only applies to the internal Database. The external Database requires Oracle 10g/11g (no IBM DB2 or Microsoft SQL Server 2008) and does scale very well when it has enough memory. (Up to thousands of virtual machines)
As linked mode is based on Microsoft Active Directory Application Mode (ADAM) to synchronize data across multiple vCenter Server systems it is not supported in vCenter Server Appliance.
Security Support Provider Interface (SSPI)
The Security Support Provider Interface (a part of SSO) is a Microsoft Windows API used to perform authentication against NTLM or Kerberos.
VMware Update Manager
The VMware Update Manager is only available for Windows. You can't install it inside the vCSA but you can install it on an external Windows System and use it with your vCSA.
The View Composer is only available for Windows. But it is no longer required to install it on the same system as the vCenter Server. A standalone View Composer installation works with the Linux-based vCenter Server Appliance.
vSphere Storage Appliance (VSA)
The VSA Manager plugin is only available for Windows does only work with the Windows version of vCenter.