Besides encryption what are 2 other problems with ftp on Linux systems?

Answer 1

Actually, encryption shouldn't be a problem because Linux does have secure FTP, Windows doesn't. So I don't see how this can be a problem.

With FTP, you can have problems such as redundancy (if a server does down), single sign-on, no certificate validation, etc.

Apart from that, FTP is great. Are you looking for diffences between FTP and HTTP, or between Linux FTP and Windows FTP?...