Improve Windows application deployment
I think Intune could really do with some work on the features that are required in order to make EM+S the cloud-first management platform that Microsoft want it to be. Along with some of the features that are five minute tasks in Group Policy but end up having to be implemented in PowerShell in Intune (I have no idea how admins coped before PowerShell support existed in Intune) it would be great to see proof that Microsoft realise that not every application is a nice modern bundle, or published into the Windows Store, or exists as an MSI that behaves well.
Ideally I would like to be able to use AutoPilot to deploy machines where users run as standard users, and then provide applications to them via the Company Portal that normally would need administrator rights to install. Whether this takes the form of a new service that runs in the cloud to take EXE installers and repackage them for deployment in Intune, changes to how the software installer part of the service operates, and a way of including files alongside MSI (required for some Adobe applications) it doesn't really matter. But at the moment there's a lot of things that people might assume would be a standard feature of an MS management service looking after modern Windows client devices, and they just aren't there.