I can't say I'm surprised to see people eager to point out how Windows sucks. And sure, maybe it does. However, the fundamental point you're missing is that I don't think that Windows was ever positioned as this OS that was designed for every single type of workload out there (not withstanding marketing noise). Windows is a very general purpose OS meant for general purpose 'mainstream' things. Things that hundreds of millions of people might want to do. Specialty workloads are simply not what Microsoft is ever going to invest any significant amount of time in - unless they see some money there. In that sense, Windows would probably be a far better OS if users could modify it to suit their needs, but thems the breaks. Linux seems to fill that void for some.

The disadvantage of NTFS which you point out, isn't because of a fuckup. It's not designed for your use case. You might even find Microsoft telling you that themselves here :- https://technet.microsoft.com/en-us/library/Cc938932.aspx

As to your point about productivity, I can't comment without knowing specifics. As a primarily C++ programmer, I haven't run into any Windows showstoppers that prevented me from shipping. I have run into showstoppers with their dev tools, but I see them as separate from the OS.