I have 5.0.1 on my Ipad2 and yes there is also a new version of Goodreader which implements a "Download" directory.
Fortunately its Documents directory remains accessible using Iphone Explorer, for simple drag/drop operations.
In the meantime Memory Map have "updated" their IOS app,
removing the feature for transferring QCT charts via WIFI
This company is going from stupid to really stupid.