User input for utility program
Yes, it is perfectly do-able through the serial monitor.  However the serial monitor is very very basic and you will be able to create a much better user experience using a proper serial terminal emulator (such as TeraTerm, Putty, etc) and using ANSI control codes to lay the screen out as a proper text-based application.

A useful resource is on Wikipedia: https://en.wikipedia.org/wiki/ANSI_escape_code

I have a little library that I started a while back and never finished that performs two basic ANSI control sequences - clear screen and set cursor. You can look at it to see how to perform ANSI control codes: https://github.com/MajenkoLibraries/ANSI