Custom control has full toolbox support but we cant add user control in toolbox. Custom control has a dynamic layout but user control has a static layout. Custom control defines as a single control but user control defines a set of control. Custom control is more flexible compare to user control.
Custom control directly added into toolbox but we can not added custom control in toolbox, custom control's main concept is reuse ability , custom control added from drag and drop but user control first register and then use, user control easy to create but its very complex to create custom control