I had problems in the past with Nautilus being invasive on some desktops, namely XFCE, when it used to compete with Thunar for the desktop, but not in elementary.
On the other hand I don't think it's "better" than Pantheon Files; and the more desktops I test, the more I believe that "each its own" is the best philosophy.
I had tried to avoid installing it, especially since I like the clean elementary OS desktop with just a background and I don't need folders and files on it, but in the end it's there and I see no big problems with that - and it brings a lot of features that I personally only need from time to time, like a proper window for the searched files, customizable columns, integration with online applications, etc.
The most notable problem it brings in my case is that it is adopted as default file manager by Firefox downloads list ('Open Containing Folder').
I also think that having a secondary file manager is a good idea. Is using Nautilus risky? What are the risks?