I'm using Transmit for many years but recently change to CyberDuck because of the following:

When FTP copying large directories with many files (12MB) Transmit often does not copy all files because of permission problems (the same files copy perfectly well with other FTP clients)

Transmit then stops the whole transfer process and not just skips the files it can't copy so you have to baby-sit the whole transfer which is also reasonably slow.

If you "replace" files with Transmit it does not make the files the same permission as the replaced files which means a lot of manual work afterwards.

When you choose the replace option Transmit will actually first delete all files in the particular folder and then write the new files, this is not a replace but a delete first and i lost my config files from my shopping cart because of this.

The Sync option also does not work for me because of permission problems (again this files are transfered without a problem with any other FTP client I tried.