To sum it up in a sentence... It's a repeater that has an integrated site controller in it.
SmartZone sites which are not IR sites utilize a central controller (usually an MTC3600, but back in the day it was a 6809), housed in its own cabinet or rack, which is interconnected via cable to all repeaters at the site. In this manner you have better control of the site and its operation, especially if your ZC link is lost. For example you can run Simulcast whereas you can't with an IntelliRepeater. Though with an IR you can do Voice on Control.
The site controller is then controlled by a master controller that is normally not located at any radio site. It's called the Zone Controller. It passes down operational commands, and does many, many other things.
-Wayne