I'm going to answer with "No", as in I can't think of any good reason you shouldn't be able to use Nautilus or Nemo or any other file manager that you'd like.
The only thing I think you would lose by using Nautilus is that it doesn't use our Contractor API. So apps that install Contractor extensions (also known as contracts) won't be able to expose those ...
I disagree with your perception of Files, which I consider the best file manager around.
My recommendation would actually be to install Freya which comes with the much improved version of Files.
If you still want to install another file manager, it's as simple as:
sudo apt-get install <your-choice>
Nothing bad will happen with any extra file ...
The .desktop file for nautilus by default shows only when the desktop environment is Unity or Gnome.
To show Nautilus on slingshot you'll need to edit the desktop entry.
Edit the file /usr/share/applications/nautilus.desktop with this command:
sudo -H scratch-text-editor /usr/share/applications/nautilus.desktop
And then change the line OnlyShowIn=GNOME;...
To replace file manager in freya:
Install other file manager, for example nautilus.
sudo apt-get install nautilus
To distinguish between Pantheon-files and nautilus, and to show nautilus in applications launcher:
sudo nano /usr/share/applications/nautilus.desktop
In [desktop entry]:
Change Name and OnlyShowIn entries to
Files does have a search facility - you just start typing or press <Ctrl>F and type into the pathbar (which doubles as search entry). The first results returned are those found in the current directory. It also returns (grouped separately) results found in subfolders of the current folder, in bookmarks and in recently used.
However, if you wish you ...
Figured out the problem, the command to hide this window is gsettings set org.nemo.desktop show-desktop-icons false.
EDIT: And to fix the desktop instead of disabling it, I just followed this guide and everything works: https://elementaryos.stackexchange.com/a/3841/7699