I think you are missing a fair bit of the other commentary in the article.
While increasing speed, it also increases traffic by multiplexing communications, which would further hamper networks.
Stateful systems aren't equipped to handle distributed state, thus pretty much any system that isn't an endpoint of a MCTCP connection is useless at doing anything besides simply forwarding the packets.
What I will agree with you on the whims of corportations is regarding the research on "side channel attacks." I don't really understand why being able to infer throughput, congestion, packet delay, etc of other ISPs is an issue. None of that information sounds horribly proprietary, but what do I know.