I've thankfully never seen a Windows Server with Flash, Reader, iTunes or VirtualBox installed, sounds like a security nightmare waiting to happen regardless updates.
I also see lots of insecure and outdated applications running on Linux servers, especially Wordpress, Drupal, myphpadmin, cPanel etc. Heartbleed and Shellshock themselves are still not patched in a good percentage of servers.
I run a few windows servers maintained via ansible. There is a protocol called winrm built that is functionally equivalent to ssh for the purposes of remotely controlling a box. Ansible uses winrm to provision. Beyond that, chocolatey.org provides a complete package management solution as long as you are looking to install popular free (as in beer) software. Also, you need to learn powershell to do anything useful. It's painful but I have to sit back in awe at the extent of the APIs available to you from the powershell prompt, each one hand crafted by a Microsoft employee. Pretty much anything you need to from a OS configuration perspective can be done in powershell pretty easily.
Once you get over these couple of things it's not terrible. (though I of course widely prefer linux)
I think one can hardly exaggerate what an improvement over cmd.exe PowerShell is. Even if I really hated the outcome, these days PowerShell is just too damn useful to ignore as a Windows admin.
One thing I am seriously disappointed with is the documentation or lack thereof. PowerShell's Get-Help/man cmdlet is admittetly nice, but compared to the kind of documentation you get with Perl or Python, I am left underwhelmed.
I also see lots of insecure and outdated applications running on Linux servers, especially Wordpress, Drupal, myphpadmin, cPanel etc. Heartbleed and Shellshock themselves are still not patched in a good percentage of servers.