I think we should just stop using commas and newlines and start using the ASCII unit separator and record separator. It would alleviate most quoting and escaping issues because those two rarely appear in actual text.
However, many terminal mode applications intercept those keys and expect them to be commands rather than data. Often there is some kind of quote key which you can press first. In readline and vim, the quote key is Ctrl+V. In emacs, it is Ctrl+Q instead.
GUI applications are more variable. But vim and emacs still support their respective quote keys in GUI mode.
And if you have to type this a lot, you can modify your vim/emacs/readline/etc configuration to remove the requirement for the quote key to be pressed first.
In this sense sticking to a relatively common separators is good, because they encourage you to do the right thing from the start.