We are in the process of rebuilding our vCenter server and are evaluating if we should go with the appliance. We have reviewed the relevant KB articles to determine that all of the services we desire are supported with the appliance.
We are running 20 Hosts and 1000+ VMs. This is well within the supported size limitations for an embedded database on the vCSA.
Right now I see no reason to not move to the vCSA, but I'm wondering if there are any gotchas that I should be concerned with.
What do you all prefer/recommend?
I recommend you choose the option that meets your today and future requirements... I personally prefer Windows version, even if VCSA meets my today requirements, but sometime the customer meets the project requirements, for example: request Linked Mode feature, and we know that we cannot migrate from VCSA to Windows versions directly.
This blog post shows some interesting points: http://www.viktorious.nl/2013/01/18/windows-vcenter-server-versus-vcenter-server-appliance/