The creation of the first round of .desktop files was automated, and as I have not dealt with the gtk2 Mplayer in a while it is most likely that the mplayer.desktop is the file that is from the upstream source, while the one with the extension name is the one created for TC.
I have caught flak at one time for changing or removing the upstream .desktop files to make a package more TC friendly. But I will look at those files and perhaps merge them into the MPlayer-svn-gtk2.desktop file.