Some ways Windows core OS could be improved:
POSIX filesystem semantics, including removing/renaming open files (continue access until closed), transition away from mandatory file locking by default, transition away from carriage returns in text files (fix notepad, start changing tools to default to leaving the carriage returns out), switch to UTF-8 encoding for unicode by default for filenames and contents (instead of 2-bytes-per-character), transition to case-sensitive filenames (when most people use GUIs instead of typing names, why have the insensitive complexity in there...), etc.
Fix it so POSIX api functions are no longer treated as bastard stepchildren - implement them in the core, and emulate others.
Include a good, standard scriptable command line interpreter by default, where it can be counted on to be installed. /bin/sh and associated commands would be a vast improvement, and it wouldn't be hard support command line editting ala bash or zsh as well.
I could go on for some time, but maybe you see the pattern. Summary: Keep the fancy end user GUI stuff, but fix the underlying foundation.