1. It would be great if subdirectories could be shown in order of the most recent CONTENTS, not the creation date of the subdirectory. I understand that would require WinSCP to scan the contents, but it would do a better job of that than I do.
Thanks for your suggestion. I have added this request to the tracker:
Bug 2119 – Optionally sort directories by last modification of their contents
You can vote for it there.
1a. Failing that, at least they could be alphabetized even if I display files by date changed.
This is tracked already here:
Bug 1024 – Option to always sort directories by name
2. It would be great of Synchronize also synchronized subdirectories.
It does. If it does not work for you, please give us more details. (screenshots, logs)