FYI, transmission-cli is considered deprecated by the Transmission developers. Using both transmission-daemon and transmission-remote is the recommended approach. Actually, transmission-cli uses transmission-daemon internally and they share the same configuration. transmission-cli is still useful for one-off downloads, but I still prefer the recommended way because I'd like to seed older torrents some more time.
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.