Found this:
MSI (s) (70:54) [10:12:00:862]: Invoking remote custom action. DLL: C:\Windows\Installer\MSIF88D.tmp, Entrypoint: VMGetLocalSQLDBTCPPort
CustomAction VM_GetLocalSQLDBTCPPort returned actual error code 1603 (note this may not be 100% accurate if translation happened inside sandbox)
Action ended 10:12:00: VM_GetLocalSQLDBTCPPort. Return value 3.
This should indicate you have not enough permissions on installing/upgrading all SQL Express features. Are you using local administrator account to install it?