Login to Skype from terminal or any other way

The skype.desktop files are not meant for you to run. To invoke skype you should be able to simply type skype in your terminal or run it via the full path here:

$ /usr/bin/skype

Files that end in a .desktop are configuration files for your desktop, not for you to execute directly. See here for example:

$ more /usr/share/applications/skype.desktop
[Desktop Entry]
Name=Skype
Comment=Skype Internet Telephony
Exec=skype %U
Icon=skype.png
Terminal=false
Type=Application
Encoding=UTF-8
Categories=Network;Application;
MimeType=x-scheme-handler/skype;
X-KDE-Protocols=skype

You could try using gnome-open ./skype.desktop or xdg-open ./skype.desktop. These used to work, but there appears to be a bug that's been present for some time, which breaks these 2 commands ability to process .desktop files. See this AU Q&A titled: Running a .desktop file in the terminal for more on this.

exo-open

Using exo-open ./skype.desktop worked for me. exo-open is part of the Xfce DE, but will properly invoke the .desktop files.

$ exo-open /usr/share/applications/skype.desktop

gtk-launch

Using gtk-launch skype.desktop /path/to/desktop/file also works.

$ gtk-launch skype.desktop /usr/share/applications

Command line login

If you take a look at the output of skype --help:

--pipelogin     Command line login. "echo username password | skype --pipelogin"

So you could achieve what you want like so:

$ echo username password | skype --pipelogin