What I heard, from a guy at IBM, is that companies don't switch to linux because installing 3rd party software is difficult. That's not an issue of retraining though, that's an OS problem.
IME of having had to manage several hundred Windows XP workstations installing 3rd party software was a pretty big issue on Windows as well. From having to verify if works with restricted permissions, to processes to automatically detect machines with out of date software to finding ways to create automated silent installs, it was a good amount of work. Now I'm curious to see how the required effort would compare on a Linux network.
I've deployed both setups, and support issues went way down compared to Windows. The biggest recurring problem with the NFS root setup was hardware failures, but the "fix" there is to swap out the machine, which takes 5 minutes, and the user continues to work. Without having to store files on the local machine, by having NFS home directories, there's no need to copy files over to give someone new hardware either. With standalone machines, the backup strategy is even easier also, because you KNOW the user can only write to their home directory.
The hardest part of the NFS root was going through and changing all the configs to not require local write access (like for logging) or having it mount a ramdisk scratch area, and if you're experienced with Linux, this shouldn't be problem. I know there are projects out there that are supposed to make this easier and do a lot of work, so it may be even easier now.
But I see what you are saying. The Microsoft provided Windows software maintenance environment is really far behind every Linux distribution. If you have a network of non-mobile machines that mount root via NFS, the work of the admin to install hard-to-install (because it's not available as a package) software doesn't necessarily even require creating package -- you install it on the root. I did this with some one-off stuff we needed that ended up in /usr/local. Voila, everyone has it. And while we all know this kind of software management (packageless) leads to a "messy" system, it's actually easier to pay off that technical debt because you can spend time later to provide a whole new, cleanly managed environment for your NFS root users WITHOUT causing them any downtime at all to do the upgrade. In a properly managed environment, the apparently problematic 3rd party software is just that: apparently problematic. You do the hard stuff ONCE, and that scales out to X number of machines (mobile or not). With Windows, you keep doing the hardstuff over and over and over because each machine diverges and there are so many things you need to touch during the install, and even things like installation are not nearly as automate-able as they are in Linux.
What would be really interesting (and I care about this not very much since I don't do even small Windows network deployments anymore, nor do I have plans to do so in the future) is some kind of installwatch style system for Windows, that re-packages installed software, installed with setup.exe, into, let's say, RPMs, including {pre,post}-install scripts that modify the registry (this is possible, I've used tools that do registry diffs). You'd have to have a clean master Windows machine to do this properly (easily solvable with virtualization), but it could be the difference between night and day when managing Windows installations compared with Microsoft's massive updates and each vendor's own installation method.
I think the bigger problem is the availability of 3rd party software for linux to begin with. Installing it is a minor detail. (Here "3rd party" means something outside of your distributions package management system, ie proprietary.)
so, yes it seems that the avalability of third party software and the "cryptic" way of installing things has them confused.
the average person might know which steps to take to get to their email, but not have understanding of what each individual step is actually doing or why it is necessary.
One of the main barriers to Linux adoption is the fact and/or perception that it requires a lot of retraining. So now that we have the fact and/or perception that moving to Vista requires retraining as well, then Ubuntu becomes just another alternative.
I've dealt with plenty of situations where Windows is the sensible choice and plenty where Linux would be. And I have no problem with someone considering the options and choosing Windows even if I'd personally have chosen Linux. But often Windows is mandated by some executive who seems to consider a computer using Windows to be as necessary as a computer using electricity; that's just what computers use. In most places it would still be a major coup for Linux to even be CONSIDERED as an alternative to Windows, even if it was rejected.
I actually don't believe that moving from XP to Vista would have required much retraining. But I'm happy to see that Vista's perceived problems have led to large organizations at least looking at Ubuntu as an alternative, whether they use it or not.