When you need to troubleshoot a failing install, it is often useful to use the policy hive rather than the command line to catch things like repairs and multi-package installs.
Existing MSI packages should be deployed as they are. If customization is necessary, a Transform (MST) file should be used to introduce that customization.
Wise Package Studio's SetupCapture application has a number of configuration options which can affect the quality of the resultant package. I will discuss them here by the option description.