I've not used Linux much on the desktop, and haven't used newer distros like Ubuntu at all on the desktop, but one problem I remember from messing around with Debian a few years ago was documentation and standardisation. That sounds like two problems,
but let me explain...
I'd wonder how to do something and find some documentation about it, either in the Linux distro itself or on the web. That documentation often didn't match up to my system. It'd tell me to edit a config file in one place when it was somewhere completely
different or didn't exist at all (because a completely different system was in place for that feature).
That's true to a degree with Windows as well... Not all documentation applies to every version. But it seemed a much worse problem with Linux, back when I tried it. It was especially frustrating when man pages which came with the distro didn't apply to it.
I think it's also worse for Linux vs Windows because in Windows you can find a lot of settings just by clicking around in the UI, and didn't have to find docs to do things as often, but newer distros like Ubuntu may have evened things up there.
From what's mentioned in the article, I'd say that Program Installation is better on Linux than Windows in some ways. (It's also more complex in other ways, mainly due to all the needless differences between distros, IMO, which touches on what I said above.)
A friend of mine is a big Linux user & developer and often bemoans the fact that Windows lacks a package managment system. I think he has a good point. It'd be brilliant if there was a central, standardised way to install and update all components on the
system, not just the Microsoft ones. It'd also be great if vendors could specify dependencies of their installers without having to actually include them, and have the OS handle downloading/updating/installing the dependencies as needed.
I'm sure there would be some problems with vendors using the packaging system in a dumb way but it seems to me that's one thing Windows could definitely take from Linux. It'd be good for developers & end users and help make the platform more stable/secure
by keeping things up-to-date.