I think all your points are valid and the only thing you can do is way those pros and cons to see what is of value to you.
For me portability and battery life is key, while the netbooks are small and easy to port, they are not as convenient as an eBook reader. See I'm more of an opportunistic reader, I just don't have a lot of time to sit at home and read. Having the reader with me I can quickly sneak in a few pages when there is down time.
I have a PRS-505 and carrying it in my back pocket is something I could never do with a netbook.
However right now the eInk experience is no where near as rich as reading on a PC. The GUI are just so much more efficient and the software to read is just so much more powerful. If you read mostly at home and heavily annotate I don't think there will be an ereader that will compete. I think the eInk reader market still have a lot of maturing to do, it's still in its infancy and as the devices grow. Your one of the few people that read eBooks similar to me which is mainly for learning and not leisure. And I feel that most eInk are still lacking. For us maybe Microsoft next ebook reader might just be the sweet spot, though they are not calling it an ereader.
However on an aside, most of the stuff you talked about being able to do on your netbook I can also do on my BlackBerry. Maybe buying the netbook was the mistake
