Some compare this to embrace and extend. Some IE features such as XMLHTTPRequest that Microsoft added to the web actually made interactive web possible for things like messaging apps. Instead of balking at Microsoft's ideas, why not adopt them into open source projects? If microsoft had not adopted Web technology it would have instead made its own entirely proprietary protocol. I dont know, it sounds like its much easier to emulate a few Microsoft extensions to an open protocol than to try to emulate an entirely proprietary protocol. Why not emulate Microsofts extensions instead of just complain? Thats what doesnt make sense about the embrace extend argument, if they make entirely their own proprietary protocol, does that make things easier for you to support? It was a while before Linux could support additional filesystem permissions like inherited permissions and a seperate create and modify bit, does it today, even, features found in Windows for some time.
Fortunately much of Linux userland is under GPL so if Microsoft does make any change to a Linux userland tool, it would have to contribute it.
I am undecided on the effect this could cause. On one hand, it might make it easier for more people to get used to using Linux apps as a stepping stone to going with a Linux system. On the other hand, it allows people to get a Linux userland without the Linux kernel, perhaps reducing usage of the Linux kernel.
Instead of working with Microsoft. I think Canonical should be working with Dell, Lenovo, HP etc to get Linux to support more PC hardware adn get Linux installed as an alternative on off the shelf computers. These makers could also fund WINE and a Windows driver compatability layer for Linux, which would eventually payoff in freeing them from MS royalties.