Goodreader is an amazing app for everything from file management, to PDF annotation and it will open a large number of file types that you might otherwise have difficultly viewing on an iPad. It isn’t free, at £3.99, but it is very powerful and hard to beat as an all-round app (app store information here: https://itunes.apple.com/gb/app/goodreader/id777310222?mt=8).

Here is information about the annotation tools available in the app: http://www.goodreader.com/gr-man-view-pdf.html#annots

However the really helpful tool for difficult-to-read PDFs is the extract text from PDF function, which allows you to define your background colour and font style preferences (called PDF Reflow): http://www.goodreader.com/gr-man-view-pdf.html#reflowThis is particularly helpful for increasing the speed of reading PDFs but allowing the user to switch between a more readable view and an annotation view.