What about good old scp?
scp file.txt user@host:/dest/dir/ scp file.txt user@host:/dest/dir/rsync -zvh file.txt user@host:/dest/dir/
So many ways to do this :)
rsync -n -avh --progress source destination:~/asdf/ for a dry run followed by ctrl-p, ctrl-a, alt-f, alt-d, alt-d to remove the -n flag and then execute that for the real thing.
Occasionally though, I'll also use sftp if I'm just pulling one thing - perhaps even after sshing to the remote machine.
For all of these, SSH keys should be set up (and desktop logins secured) to make life easier.
As for Android, adb push and adb pull -a seems to work better than mtp:// or AirDroid in my experience.
rsync source destination will plonk the entire source directory and put it inside destination as a neat bundle.
rsync source/ destination will take the contents of source (but not the directory source itself) and plonk it in destination
I found the info page a little dry but it does describe it succintly:
rsync -av /src/foo /dest
rsync -av /src/foo/ /dest/foo
If in doubt though, just chuck everything into the destination ~/temp/ or ~/asdf/ and sort it out later.
To be honest though, most of the time I just use fish shell's autosuggestions to guide me along.