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A word of caution: we're still living in the early-adoption phase of eReader technology. If you buy an e-reader today, expect it to be antiquated within one calendar year. If you can wait on purchasing an e-reader, if you do not have a lot of money, or if you are not an avid reader, I would suggest holding off for now. If you can't wait, if you have a lot of money, or if you are an avid reader, then it may be worth the purchase -- so long as you can handle the fact that a better model will be out this time next year.
Aside from that ...
I don't own an e-reader.
I have friends who do. Two own Kindles. One owns the Sony device. None own the Nook but several have voiced interest in obtaining one.
Everyone seems pretty satisfied with their purchases. The Kindle owners insist theirs is best. The Sony owner insisted his was better than Kindle 1.0 (he was an early adopter!), and is now looking towards Nook rather than Kindle 2.x. I think that you will be satisfied with whichever one you choose. None of them are perfect, as you have already pointed out. So find the one whose flaws irk you the least and go with that, I would say.
There's always going to be new ones every year and from what I'm hearing, the next step would be color E-Ink technology but I'm not sure exactly if that would even be a selling point for me since manga scans are usually in black and white anyways. Thanks for the input on your friends purchases, I'll keep an open mind on all options.