I have had this question for some time and now think I've found the answer - so I'm making this post to help others out. Others can test the idea and see if it works for them or point out the disadvantages/advantages of my suggestion.
When you use the Window GUI "Shutdown" command, it doesn't really seem the Surface RT ever fully shuts down but instead will periodically enter Connected Standby mode and if the device gets overly active in this mode, it can rapidly drain your battery. I have used the admin Command Prompt "powercfg /sleepstudy" to see what's going on during such "shutdown" sessions. I found activity of the Marvell network adaptor and associated app activity with updating over the Internet seems to be the major culprits of battery drain.
The 12/10/13 Surface RT firmware update may have helped me. But basically I've found the following has allowed me to ~completely shutdown my Surface and prevent battery drain when I just have it lying around. I enter Airplane Mode (Wi-Fi and Bluetooth off). I turn off the Live Tile of the Tile Time app (which "powercfg /sleepstudy" showed can chew juice in Connected Standby), then I use the admin Command Prompt "shutdown /p"
Since doing the above, my Surface RT always shows the same battery level on starting up again after many hours as it did when shutdown by Command Prompt as shown by "powercfg /batteryreport" The device remains in SUSPENDED state when shutdown and does not enter Connected Standby mode.
Obviously if one does this, one loses all the advantages of Connected Standby, i.e., updates and maintenance performed while you are not using your Surface RT device.
One could say just leave your Surface RT plugged in while you're not using it and you won't have to worry about your battery discharging in Connected Standby. However, keeping your battery charged above 80% is NOT conducive to a long battery lifetime usage.
I've posted further advice/description of my Surface RT battery care towards the bottom of p.8 of following thread:
and I've previously described Sudden Discharge issues with my Surface RT at length in the following thread: