It won't allow you to transfer "Ratchet & Clank Tools of destruction" for example. It often chockes and freezes when transferring games that have a massive number of folders\files.
Also, it gives errors (as with R&C) in the log but doesn't actually stop the transfer so unless you check the log (which only holds the last couple of hundred transfer entries) you will be left with a non working backup. For example R&C folder is about 23GB. With Filezilla, I had a folder less than 5GB...but it carried on transferring and the error was hidden away and only noticable when I looked for it after doing that game again.
Errors are one thing, but errors that you have to track down can be a time wasting problemd down the line if you dont even know there was an error. Hence after using WinSCP I wouldn't touch Filezilla with a 10 foot barge pole.