Unless you think your wife, or you, want to consume precious reading time with futzing with formats or hooking it up to a computer and side-loading, I would go with the Kindle, not rooted. It sounds like you are already interested in the Amazon bookstore, and library reading. Both work well with the Kindle.
This forum is filled with tinkerers because that's what we do
But for someone who wants to read, not goof around with formats and downloads and sideloads, go with the simplest method possible. And Amazon has that pretty well done. B&N is a close second, but selection remains an issue with them, and Amazon is working hard to make sure they have the biggest selection, period.