For help generation and better error handling, Pod::Usage has been in my toolbox for a long time. It will pull the help right from your perldoc POD. (Which you were hopefully going to write anyway, so it's no extra work.) It is configurable as to which sections it will pull and display when help is needed.
Your point #2 has me confused. Why is that important, as long as the interface is well designed and documented?
Point #3, there are indeed a lot of features from Pod::Usage and the plethora of Getopt:: modules you've seen. None that I know you need though. (And none that I use on a regular basis.)