As a fairly new NOOK owner myself (and a tech-geek and tinkerer) Hopefully I can help out on this one.
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1. Rooting...... Read a bit about rooting the OS on these devices. I'm definitely amenable to this idea, but, can you even root a Nook Classic?
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Yes you can root it. I have firmware v1.5 and SN10036. However Rooting that combination is, at present a royal pain in the backside for only a modest improvement in capabilities.
Read the instructions here and UNDERSTAND before you even attempt. In all honesty though I wouldn't bother as I think that "the juice isn't worth the squeeze".
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2. Cover/protective case......are these really recommended?
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I vote yes. Of course
I made my own so that gives me a different perspective.
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3. PDF support.....I imagine that PDF support is limited on these, and on the 6" screen, probably won't look great.
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I agree completely. PDF support works but it's tiny tiny tiny. You would be FAR better off translating any PDF files to ePub with the free
Calibre software.
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4. Since this will have WiFi, I'm assuming it has a web browser built in. I also assume, that since this is a black and white e-reader, the web browser is probably crap.
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I've tried the browser...I found it too annoying to use on the NOOK Classic and have basically only used it to access better dictionaries online. The rest of the time my WiFi stays off actually so that's as much as I can tell you about the browser.
One other thing to note is that although the NOOK has the storage capacity for several thousand books (or tens of thousands of books with an expansion card) the OS chokes at somewhere around 1900-2200 titles. Additionally the cataloging method on the device is pretty cumbersome at much over 200-300 titles.
I had initially intended to have my ENTIRE library "in my hand" but the NOOK simply isn't ready for that. However I was able to come up with a different plan, using Calibre on my PC to organize/catalog/locate my books and putting selected ones on the NOOK to read. So far it's worked pretty well though even with 1200 titles installed I still came up with a reference work or two that I didn't have on hand when I wanted them <sigh>.
So these days my operations are basically my PC+Calibre= "The Library" and the NOOK="books checked out to read at the present time". Actually it's working out pretty well so far.