Transfer of lot of small files is always relatively slow. You can use transfer queue to parallelize the transfer to optimize it.
https://winscp.net/eng/docs/transfer_queue

Hello.

I thought rsync / Synchronize on WinSCP would be relatively fast, except for the initial indexing, for many small files. Maybe not as fast as tar compression and sending over ssh, but fastest when using WinSCP for small files.

I've tried disabling "Optimize connection buffer", enabling "Compression", using arcfour and using "Synchronize", still the transfer is awfully slow.

How can I optimize WinSCP for small files?