I am testing the Amazon S3 feature, and it would be really nice to have these addons
Master password that the user can choose to access the S3 accouht (instead than the complex access key)
Possibility to edit files and folders permissions
Both features are available in "S3 Browser", just in case you want to know how they are done. I would gladly fully switch to WinScp if they where available there too.
another nice addons would be multi-part uploading for S3, I have not tested uploading really big files yet, but in the past they used to fail unless using multi-part uploading