I was greatly disappointed too when I found out about transmission-cli's deprecation, but I have since found and replaced all uses of it with stig[1] which, for me, does the same thing and more.

[1] https://github.com/rndusr/stig

You can still do that

   $ transmission-remote -a one.torrent two.torrent

You could also check out rtorrent: http://rakshasa.github.io/rtorrent/, but I remember reading that development has stalled on that project.

aria2 can download a torrent from a magnet link given as CLI parameter.