In case you haven’t seen it, at Ignite in September we introduced the concept of co-management with Configuration Manager and Intune both managing the same device. https://channel9.msdn.com/Events/Ignite/2016/BRK2138-TS
If you already have ConfigMgr, it makes sense for now to consider this configuration to address app deployment.
An error occurred while saving the commentJulien Garrigue commented
Yes, application dependencies is interesting because some software need a package (like .net 3.5) to be installed before otherwise it cannot be installed.
By the way, Tamir, it's already possible to deploy cmd, bat, ps1 via Intune with a little trick I can give you if you want.