The posix subsystem was usable on NT4. Not so much since then. The latest version is basically a wrapper around the GNU tools and is more about Microsoft checking boxes on government forms when bidding on projects than anything else.
Cygwin is not perfect but I'd say it has far less issues than what MS offers.
Network authentication for UNIX systems relies on the insecure NIS protocol (LDAP- and Kerberos-based authentication require a third-party solution). Microsoft has released several hotfixes for Windows Services for UNIX, and at least one Security Update (KB939778). The GNU Project utilities are several versions older than the latest ones. A separate port of the up-to-date Debian utilities was started in 2007, but apparently abandoned in 2009. Several of the text processing utilities in SUA (e.g. awk) are not compatible with Unicode or wide character text files.
I can't think of one application where Cygwin would not be far more beneficial than MS's half ass attempt at being Unixy.