Transmission aborts automated shut down. My ISP offers unlimited downloads at a certain time period at night, but I don't want to wake up to shutdown my MBP 13.3 at that time. I tried to specify a certain shutdown time using the Energy Saver option.

However, I found out to my utter dismay that Transmisison needs to be explicitly closed before it for the computer to shut down.
In Transmission go to the preferences
uncheck System sleep under Network

uncheck Quit with active transfers under General