The en-route charts are an issue. Have you had any experience with Jeppesen's FD app. It is a start but is still lacking key aspects such as DME steps. To get the charts for NZ or Auz requires a subscription to the entire South Pacific at a cost of almost $1000 per year.
Scanning the en-route charts as PDF's and viewing creates problems with the size of the file and slows the iPad down. Perhaps reducing the file size, and the more powerful iPad 2 may reduce the issue but Im not sure scanned paper maps are the answer.
Jeppesens TC app for approach/departure plates is a great simple app, however there is still that $1000 subscription.
Dont quite follow you on deferring the job of certification for critical phases of flight.