Well, I did see this ticket, but it seemed to have fallen into oblivion. :)
I hope it makes it to WinSCP 5.2 (I know, too late for you anyway).
- encryption of stored passwords
Do you mean master password?
- more reliable for big transfers
Does FileZilla drop big transfers or what is the problem?
Two thing from Filezilla that I'll regret :
- easy file queue management
What do you miss in WinSCP specifically?
- tabbed sessions
WinSCP has tabbed sessions.
- WinSCP's strange GUI while transferring (this modal window with this "minimize" button)
You can make WinSCP use queue for all transfers, just like FileZilla:
Let me know if that helps.