I get a bunch of
/bin/sh: lt: command not found,
while I expect it act the same as
mapm 'ls -Alrt --color=auto $_' ls,
because "lt" is aliased to "ls -Alrt --color=auto."
Notice "/bin/sh" above. My shell is actually tcsh. All the aliases are in ~/.cshrc.
"system"-like functions in most languages use /bin/sh specifically, regardless of the user's shell, because programs cannot be expected to adapt between the different redirection commands use by sh-like and csh-like shells. Consistency is important here, if you run a shell command from a program you do not want to deal with the fact that csh speaks an incompatible language and fish uses XML, etc.
If you really want to run your/the user's shell, retrieve $SHELL from the environment and run it directly.
system $ "${SHELL:-/bin/sh} -c '" ++ mycommand ++ "'"