Keep it real, though -- reading scientific papers on iPad
mini?
I'm in the same pickle as you are: I hate PDFs and how they display on the iPads, but for scholarly purposes, you just can't avoid PDFs in many instances, no matter how hard you try.
Apart from developing your own app (and good luck in doing that -- GoodReader will be tough to beat), you have few choices other than
mitigating your suffering. The first step in that direction is to get a full-sized iPad instead of the iPad mini. It's still not A4-sized, but reading PDFs on it isn't as painful as on 7-inch readers. For the same reason, I still prefer my old-fashioned Kindle DX over the modern Kindle devices -- especially for reading PDFs, the larger Kindle display wins over the smaller display every time, despite lower contrast, resolution, etc., on the older Kindle.
PS: On the Android platform, I read praise about Repligo.