Under what circumstances is TCP-over-TCP performing significantly worse than TCP alone (2014)?
Solution 1:
I think it's actually more debated than you make it appear. There is an admittedly old, related Linux FAQ: http://www.tldp.org/HOWTO/VPN-HOWTO/
I've used a PPP-over-ssh-over-ADSL for more than 12 years, and it never failed me, so from my experience I'd dare to say that the doomsayers probably largely exaggerate. TCP over TCP is probably a bad idea with RTC connections, satellite links and other links with either very low throughput or very long delays, but for most uses it just works.
Now the true question is: why would you use TCP over TCP at all? When I've set up my PPP-over-ssh, it was largely because back then it was by far the easiest way to build a quick VPN; then I've used it ever since out of sheer laziness.
Nowadays there are practical, easy to set up tools like OpenVPN, IPSec VPNs so that you shouldn't ever need to bother you with this TCP-over-TCP problem.