I think the major thing you lose from the reader, when rooted, is B&N's "LendMe" technology where you can lend an ebook to someone else. Basically it makes the book unreadable for you for two weeks, and your friend has to weeks to read it on their device. After two weeks it reverts back to you. Not all ebooks are lendable, I don't know how it's determined which are and which aren't.
What you gain, in my opinion, is much more important. The stock Nook (and the Nook market app) have a really crappy 'library' interface. You can't flag a book as having been read, which is a major misstep as far as I'm concerned. I have several hundred books on my Nook, many of those are series which are best read in order. However I rarely read a series all the way through, I'll go away and read other things and eventually come back to the series. There is no way that I'm going to remember which books I've read and which I haven't, so I need an indicator to show me that. I'm not SURE that the stock reader allows you to read the 'back cover' on a epub book (most of mine are side loaded epubs, not books bought from B&N). That to me is another 'fail'. When I'm looking for my next book I want to read to see what they are about, to see if it matches what I'm in the mood to read.
The READER portion is fine, but I'd say that's true on all of the reader apps I've tested. They all allow you to set font size and color, and background color, most allow different margin settings, swipe to changes pages, etc etc. Some readers are really proud of their page turning animation, which is one of the first things that I turn off. I don't want to see an imaginary page turn, I just want it to flip as quickly as possible to the next page without waiting for any fancy graphics to make their way across the screen.
For me Aldiko is the best reader app currently available (you have to be rooted to use this). The main thing it has going for it in my opinion is the ability to rate a book. I rate a book when I finish it (1 through 5 stars). The rating itself means nothing, the fact that I have rated it indicates that I've read it, which solves the first problem I mentioned above. When looking for the next book in a series, I can tell which ones I've already read.
BTW, yesterday while and B&N I asked about flagging a book as read, the helpful lady suggested adding a new 'shelf' in your library (stock Nook) and moving books you've read to that shelf, as an indicator that they've been read. That would certainly work, but it puts the book on the 'wrong' shelf - IMO.