Remember WinCE? Microsoft's embedded products are not the same as their desktop products. And, no, WinIoT on a Pi will not run the same executables, it is an ARM platform which Microsoft just emphatically orphaned with their last go around. Remember the surface RT? That did not run any standard Windows executables, at the very least the executable would have to be compiled against the ARM build chain, and that isn't an option for end users of proprietary software.
Thinking about this I understand the point a couple (at least one) person has made that MS getting involved will help mainstream the non-x86 low power stuff, or at least the ARM branch, but then I remembered what happened to the exploding world of netbooks when companies started growing them to run Windows.
The netbook market disappeared, seemingly over night, and now we are left with ultrabooks, or whatever they are calling the MacBook Air class of machines now. Sure they are light and small, but they are a whole lot more than the $100 price point netbooks were approaching.
On the Pi there is a lot of similarity to the Android stuff, we have Java as an app platform. Is this new Pi really powerful enough to mix Java and ARM.net at the same time? Just the overhead of a Java VM plus a .net framework resident at the same time sounds a little bit much for any current ARM SoC with just a gig of RAM
Now if you are targeting actual IoT devices, just developing on the Pi, sure a single purpose embedded device will probably run on a Windows stack just as well as it will on Linux. I am a little concerned about MS attempting to be responsive to exploits, but then I think we will find that most people never update their thermostat or refrigerator regardless of what OS it runs, so I think the exploitability will probably be a wash.
I am more concerned that some inexperienced whiz kid, whether he be of the .net or Java persuasion, will manage to make an actually universally useful device, but not know enough about the actual requirements of embedded programming so it just works well enough for everyone to buy one, then all the non-techy people who buy it get their home netork pwned or it crashes in an untested but relatively common use case and has significant socio-economic impact on our tech dependent society.
So all in all I really don't think MS jumping into the fray is a bad thing. I don't plan on running it on anything I build, but think about it, according to the rumors Apple thought hard about buying Nest. Would you want your house controlled by software coming from 1 Infinite Loop?
Are you actually confident about running it on software coming out of the Googleplex?
The truth is everybody that doesn't read /. is gonna buy these connected devices just like they do blenders and dishwashers, and if they act up they will return them to Walmart or Home Depot or Best Buy and get their money back just like they do now with toasters, TVs, and computers.
Do you care who wrote the code embedded in that 386 running your microwave? Do you even know if it is a 386 running your microwave? Me either. I do know that at least at one point the embedded 386 family was often used for things like that, but I never bothered looking.
OK, I am down meandering and ranting.