I tried many apps but my workflow became
Notability - in classes without pdf lectures
GoodReader - in classes with pdf lectures
Pages - for word processing
Dropbox to keep my dropbox in order
iAnnotate does render pdfs faster than Goodreader, however I didn't like its interface or its file management/syncing system. Its useful to review pdfs you create in goodreader.
One huge advantage Goodreader has is that for handwriting it has the zoom box and the handwriting system in general is very smooth.
You might also want Keynote for presentations. For science journal articles I normally use Mendeley's Paper on my Mac however the Ipad version is lacking so I kept the Mendeley Folders synced to dropbox and synced those onto Goodreader.