I don't think there's a feeling that WinSCP is infalliable, it's just that Martin's not a TCP/IP expert (I don't think, anyway) and I don't think he has any ideas what else he can reasonably do to make WinSCP faster. If you (or anyone who reads this thread) have patches for WinSCP or PuTTY that improve transfer speed, send them to the PuTTY authors or to Martin. I'm sure they'd be happy to see their software made faster.
For me, PuTTY (and by extension, WinSCP) has never compared favorably with other software in terms of throughput. But the user interface of PuTTY and WinSCP is head and shoulders above everything else, so I use them anyway.
[Martin, sorry if I'm putting words in your mouth here.]
Oh, I understand that (the first paragraph, but there are seems to be some sort of feeling that just changing the encryption algorithm is a silver bullet, or that the problem is far less widespread that it is. I'm not saying it's an easy to solve problem, by any means, but 80% slower than comparable apps feels like a configuration issue more than anything. And it's not that it's slow -- it's obvious that it can perform faster, but it performs at something of a ratio to what it seems like it should. (e.g. people that should be getting 8MBps get 1-2 MBps, people that should be getting 700Kbps get 100 KBps, etc.)
As for the second paragraph... that's where I'm at, too. Sure, I can use the command line tools that are faster and, in fact, I may. But for the others in my team, they can't so there isn't much I can do for them other than try to figure out if there is some sort of configuration issue causing the slow down.
On issue with forums is so often questions go unanswered in writing because the original person asking fount the problem and thus never checked back. I'm hopeful that someone might have an answer.