leproide I would suggest a small amendment to your idea.
How about when you first connect to a new car it offers you the choice of a full backup, as
vwjap said doing a full backup currently takes between 30 to 60 minutes dependent on internet speed. If this car is yours or you are going to be looking after it then you would probably say yes please.
However if you are a small garage then you would not want to do this for a new customer (both because of time and you dont have exclusive access to the car)
If like me you help out friends every now again just to run a scan I would not want to loose that time
However i agree it would be great if it could offer the reminder to do it.
The currently download process for full backup gives you one file so its very easy to do a self compare using excel (thats my preference as I can then update the file to record what and why i changed stuff) or other tools but dont forget you have your history to tell you all the changes you have made.
With regards to individual control unit backups there is a bug in the release that means you cant currently just send that backup (I have raised this bug on the beta testing area) but you can do a work around so you only email the one extract.
Non of this is perfect i agree but as always with OBD11 its about what gets done first and personally I would much rather they sorted out the live data issues.