I have been using GoodReader for academic reading on an iPad mini during the past couple of years, I find it well worth the investment with it’s highlighting, markup and note taking features, etc. I tried an Amazon device but just couldn’t figure out why they are so popular. The only issue I have with GoodReader is the extreme slowness of PDF loading from iCloud, but my workaround is to copy all PDFs to the device manually.
It probably doesn’t help that it’s an old iPad mini - the original version 1! It still makes a great e-reader though :) I do have the Kindle app installed for a couple of Amazon e-book purchases too. I also still use it for reading e-mail (including TidBITS) and the odd game… FlappyBird anyone?