Hi SNH, while I agree wholeheartedly with your sentiment we have a fundamental problem with making inroads into anti-throttling systems, that is simply lack of programmers.
Whilst many ideas have been kicked around even the most simplest are going to have their work cut out to ensure existing client compatibility, it could be possible to have an add on that initiates an extra exchange between the two clients as a precursor to initiating an encryption layer after the initial connection is obtained but this could be too late with some of the current throttling systems, many trigger on the simple sequence "GET" sent with other information in plain text
Whilst this remains as it is in a non encrypted state they are free to throttle and do as they please, on the flip side they could always block unidentified encrypted traffic as a precaution as some are doing to bit torrent clients currently, so as you can see we really need a team of good brains on this with time to experiment on ways to enhance file transfers without breaking anything, a challenge to even a sharp mind.