I guess the question is why does the stock NOOK not meet your needs? You mentioned wanting to run the Kindle app on it. Why? Do you have Kindle books already? Are some books you're interested in only available from Amazon?
You'll be able to root it, but it's still an eInk device. What type of navigation and performance capability do you anticipate it having? Do you have specific apps you want to run on the NOOK (besides the Kindle app)? If so, do you know if they work adequately on it?
I can't compare the rooted NOOK to the Kobo. Here are my reasons for preferring the Kobo over the stock NOOK.
As far as I know, there have been no enhancements to the stock reader app or stock library management on a rooted NOOK.