I own a Kindle 3 WiFi/3G.
I do wish there was more manual options for sorting files, but it's not bad. It's annoying that you have to hack the thing to put your own files into the screen saver. Don't know what other devices are like, but I dislike how the Kindle overprotects users from themselves. I prefer detailed, functional options, something the Kindle lacks.
Tactile keyboard is one of the reasons I got the Kindle, and I hope the next time I get an eReader I can still get one with that. I also found the Kindle 3 appealing to the eyes, whereas the e-ink Nook is sort of ugly. LCD was a deal breaker for me, I'm not getting a device that makes reading harder on my eyes. The 3G connection is a great addition, so getting any e-reader in the future I would want that again. I don't know which Nooks have that option.
As for the ePub format I've never needed it, but AcidRainLTE is correct.
I love the Kindle, the one significant knock is in the software not allowing more personalization. In general that doesn't matter much, but it is disappointing, particularly when you first get it. My understanding is they're ok with you removing the locks, but you lose the ability to receive automatic software updates.