I suspect this is a bug in the debian packaging.The Type in /usr/share/applications/e16.desktop indeed has to be Application, whereas (I believe) it must be XSession in /usr/share/xsessions/e16.desktop.
The original e16 package does install the two different e16.desktop files. -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org