Same here. I love my Nook Color. I bought it specifically to root it. I own a Kindle which I would much rather read long-form fiction on. The Kindle is terrible for reading academic pdfs and programming books. That is at least 50% of my use for the Nook, the other 50% being general android apps and web browsing. I haven't even opened a book on it yet.
How smooth is the Nook Color for navigating around an academic PDF? When I've played with one inside the store, it seemed a little jerky when zooming on the Nook Color manual PDF.
I think that the stock Nook Color app is not that great for reading pdfs. I use the Adobe one and I've tried one other pdf viewer (that I can't recall the name of now), and they were markedly better.