Endomondo without autopause
Technically, it's highly possible, since you can export your routes to .gpx files and manipulate the timestamps. 

A .gpx file is actually an xml file which is similar to html files with tags. Each tag tells you the current longitude, latitude, and the current time stamp.
You actually can edit the .gpx file with a text editor, i.e. notepad and edit the file by yourself. However, you need to know the exact long-lat where you want to "pause".