The Nooks battery life is about 5-8 days for an average reader. Average tends to mean 2 hours, so 10-16 hours. For someone reading 8 hours a day you will be recharging on a daily basis.
The K3 average battery life is one month, so you will end up recharging once a week.
Go to a Best Buy and take a look at both devices. You will be able to decide which has the form factor that best suits your needs.
EPub is not that big of a deal. You can buy books outside of Amazon that you can load onto your Kindle without converting formats. Amazon's book store is huge, the largest around, so you will probably find that you don't have to go outside the book store all that frequently.
The Pearl screen is amazing. Many folks have commented on how much better a screen it is then the one found on the Nook Classic, K2, and older Sony's. Additionally, the Kindle dictionary, note taking, bookmarking, and highlighting are all a great deal easier on the Kindle then on the Nook.
I have a feeling that either device would work for you and you already know where to find your books. Check out the devices in person and see which one feels better in your hand.
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