There are plenty of third party GPS units that work just fine with the iPad. Pretty much any of the bluetooth units work fine. You can even use an iPhone to send GPS data to the iPad via bluetooth. Airnav Pro has the capability of receiving it. I have not found a problem with the built in GPS yet even in a 5t high wing aircraft. I have encountered the problem as with all GPS units that it can't see through our heated windscreens at work which has required the Bluetooth GPS on a side window.
As for file storage, reading etc take a look at GoodReader. This will connect to virtually any online storage facility. It allows you to keep documents locally and pull down over the air whatever you have in storage. I have every available European AIP in my MobileMe cloud space and pull down the ones I need for off line viewing deleting the local copy when I am done. The plates are available from CISflight.
I use Foreflight HD when in the USA and that is really the yardstick for all navigation applications with airways and VFR charts, IAP etc but in Europe it is pretty hollow and not worth the money.
My current 'active' collection of apps that I use for work and play are:
Jepp FD & TC
AirNav Pro
Goodreader
Weather Pro HD
Aero Weather
World AV WX
FlightPlan
For online planning and filing I use rocket route which works fantasically on the iPad once you have learnt about some of its quirks!!
The iPad is not perfect but it does a pretty good job of meeting my needs and it is a damn site better than what we had just 2 years ago and saves me lugging a laptop across the world all the time.
Approach it with an open mind and you will be surprised what you can do with it.....