I work for that Windows company, and Windows is my OS of choice for pretty much everything I do on the desktop and in the cloud, with the only exception being VMs that I use for stuff that has to run in Linux (e.g., building yocto images for BB).
HOWEVER, for embedded stuff, I still stick with NETMF, Linux and an occasional foray into mbed.
The main reason is that there is still no analog for Docker-style (or even MFDeploy-style) in-field updates. In fact, there are a number of built-in measures against side-loading that work against you developing your own IFU mechanisms. On top of that, unless you pony up to get IoT Pro, it's simply not acceptable for your clients in the field to get updates pushed to them at the same time you are seeing those updates for the first time. You can't guarantee stability unless you can accommodate breaking changes in those updates concurrent with the update. There are a number of built-in impediment to starting small-but-viable with Win IoT and scaling up (you can start small, but with unacceptable restrictions) - no such impediments or buy-ins exists in the Linux world.
If we could get Docker-like containers on Win IoT and update throttling without having a big buy-in, then I'd definitely give it a second look because the tooling is otherwise superior.
I think they'll (WIn IoT) get there - they just aren't there yet.