I'm too new to recommend anything for the iPad2. However, I am surprised that Adobe hasn't already provided an Acrobat App specific to the iPad format. I guess the bad blood between Steve and Adobe is still fresh.

I am also a student who plans to use the PDF reader for text books. However, some of these are over 3000 pages and I tried the search function on goodreader which took 5-10 minutes...are any of the programs quicker (something closer to 30 seconds would be nice).

Or maybe you need this PDF tool like the iFunia PDF2Text?

Let me tell you this... If the Dropbox app has the bookmarking and annotation options, it is the best PDF reader ever! I'm such a fan for vertical scrolling.. Of course, if they have the options to manage the files and folder within the app, it will be great!

Check the iannotate, iBooks, neu.annotate, upad w/c is the best. there's a lot in the app store just search and try.