I agree. In theory.
I usually try to avoid modifying system files when it's enough to modify one user's. I remove commands from /etc/profile but don't add commands to it but instead add them to user's profiles.
Once, however, I made the same error. I replaced the system shell (/bin/bash to which /bin/sh was a symlink) with a patched version of bash3. There was absolutely ne reason to do this, as the modification was needed only be one user; wasn't quite important; the patched shell previously worked pretty well installed to my home directory, and later, installed to /usr/local/bin. It was a mistake, I admit, but luckily I saw no harmful effects from it.