Indeed. I love my iPad Mini and I use it for pdf's quite regularly (GoodReader is great for this), but it's just a tad too small to comfortably read A4-size documents, even on a retina screen. For many eBooks this is fine, but scientific papers are usually A4 and can be hard to read and annotate.

In some cases this can be fixed by cutting the margins, but aside from a certain unpleasantness I feel reading an almost-marginless document, it's often still not enough to comfortably read.

So for the most part, whenever possible, I go for ePub documents using Marvin (also an excellent app), and I print the larger documents.

It's one of the main reasons I'm considering getting a normal-sized iPad though.