Probably there is no “best” answer on this question.
However this will be depend on how many Endpoint/SIP UA under VCS and CUCM and whether or not using call escalation feature on CUCM.
If you are planning to use MCU more with Endpoint/SIP UA under VCS also planning to use VCS-E in future expansion for inbound/outbound traversal call, probably make more sense MCU to register on VCS for now.
Also if you are planning to use Multiway feature, MCU should register on VCS (and BFCP which still have few limitation while call handle by CUCM).