If you care about external storage, then definitely the Kindle and iPad are out. However, you can also use cloud services like Dropbox to expand your storage.
If you are going to use scans that are not OCRed, I would especially advise you not to get anything smaller than a 9-10" tablet, and probably Android, because iPad doesn't allow you to put in microSD cards. And even if these pdfs do have reflowable text, if they have diagrams or extensive formatting, they aren't going to look very good converted. Reading scans of documents on a 6" e-ink reader like the Sony isn't going to be very pleasant. I have the Asus Trasformer and it works well for PDFs. However I haven't tried to open really large ones.
Now, if you are going to be highlighting/notetaking, you then need to choose a good program for that. I use ezPDF Reader, but there are other ones that people like. You will also need a capacitative stylus. The one people say are the best on the forums I frequent are the Adonit Jot and the iFaraday.