They've said the initial intent is for developers to use it, not for running servers / etc (which is why they only target Windows 10 client and not Windows Server OSs).
If I can't run the entire stack I use for dev under the subsystem then I will go the other route, which is to continue using VMs. I am excited about the initial release, and the prospect of being able to use Windows for all of the regular things I do, but it's clear that this isn't ready for primetime even as a dev tool.