Well, this has been a long awaited feature in Intune which is now available in preview: deploy application which supersede a previous one.
The current state of this feature only applies for Intune package (aka Windows app (Win32)); this is not yet (?) available for MSI applications.
You can configure the supersedence during the application deployment or once it has been already deployed.
When configuring the supersedence you can select multiple application (up to 10 supersede applications) as well as choosing the uninstall the previous version