vCenter 6.0 u3 is a major version upgrade but 3a and 3b are minor patch update/bug fixes. as long as the vCenter is 6.0 U3 it will support the ESXi 6.0 U3.
I would recommend you to check the vCenter release notes to identify some of the known issues and co-relate with your environment whether those known issues are expected in your environment or not.