Operating system updates behind Transparent Proxy okay?
Tor's transparent proxy feature is at the moment a bit complicated to take advantage off and therefore unpopular. That might change in the future, because a) documentation improves; b) in the future (depending on the outcome of this bug) there might be pre-configured, ready-to-use packages; you discussed to give TorRouter such a feature #3453 (closed) as well.
You ask the user not to use Bittorrent over Tor, as the network can not handle the load.
What about operating system updates behind a Transparent Tor Proxy?
The transparent proxy feature is great, it offers to reduce the risk of leaks and offers an anonymous torified operating system. Operating system updates behind Tor are a dilemma. It's several hundred of megabytes.
Once users have an anonymous torified operating system, they use apt-get upgrade, they won't bother with offline updates, as they are complicated and possible leaks (creates signature).
So what do you suppose to do with the Transparent Proxy feature? Leave complicated, a nice addon for powerusers? Or encourage people to extensively use it? How do you want to solve the operating system update dilemma? Can the Tor network handle the load?