I agree. You still need the real charts but when planning. The facility in FliteStar to overaly the REAL charts (scanned in by Jeppesen) is really powerful.
The big issue with simplistic planning on these programs is the lack of coverage for gliding and parachute sites. Thus the use of the scanned charts.
You MUST then plot it onto a real paper chart for verification (it is easier to miss something on a computer screen than a real chart).
If find this is much faster when crossing over multiple charts or navigating complex airspace.
One benefit of these programs is the airspace is updated much more frequently than the paper charts! So using both should be safer.
You point about the class A airways seems to be true

- but the scanned charts do show them.