Hi Alejandro - If they vary in protocol, i don't think you can do much about it.
However, for the files which are in file system...you can pick them all using one channel incase the content conversion is similar..
Incase you want to handle using one channel, then executing OS commands is another option.
i.e. write a script to download the files from FTP server to local file system.
then call that script from sender channel.