Linux is a far superior kernel versus both WinNT and WinCE both in features and platform support.
If Microsoft is to be successful in the future, they should dump WinNT/WinCE and Trident entirely and built on top of Linux or *BSD/XNU and Webkit.
I really don't want there to be just one kernel or just one HTML engine in existence forevermore. Nor do I suscribe to the school of thought that says that Unix (and its variants) represent the be-all and end-all of OS design. It's absurd.
I also question your assertion at how superior Linux is. There's a reason why Android NEEDS multiple cores to run half-decently. There's a reason why my DVR takes forever to boot up. Linux ain't all that.
As for "spending money to get NT up to snuff", I assume you refer to the phone space. Microsoft is already spending money on slimming down NT anyway for Windows 8. I've heard that Windows 8CP boots very fast and runs on very small memory footprint compared to Windows 7. Since they're doing that work anyway, may as well apply that same work to the phone space.
Finally, check out this video and tell me how WebKit or Linux kernel is so superior, 'cause I don't see it: