After using my iPad for the past half year as my main reference tool, I discovered the biggest problem was that GoodReader is just not that fast for searching through files, and "flipping" is also quite slow with the page needing to refresh. (In fact, this was the original problem I had with attempting to use the Kindle as a reference tool.)
The slowness problem have been resolved with the iPad 2's faster A5 CPU. The iPad 2 is also lighter making it much easier to hold with a single hand, even for the 3G version. The iPad 2 is also much thinner and weighs much less than my Windows Server 2008 R2 Unleashed book. Besides the faster CPU and the cameras, there's really not that much difference for my uses, so I'll wait for the iPad 3.