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.Julien 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.