Here's my two cents
I am sort of in the same boat as you, and am in the market for a large screen reader with stylus note taking ability. I have a 6 inch reader (Sony prs 505) which I bought mostly for reading fiction, but I have found that I actually read a lot of pdf textbooks on it as well as journal articles. The reflow works great, as most of the articles I read are text based pdfs. I have been pleasantly surprised to find that some scanned texts (if they are scanned with character recognition) can reflow as well. Mind you, the journal articles I read aren't very graph or picture heavy articles. I would still like a large-screen reader, but for now I am very pleased with my 6 inch reader. At any rate, if and when I do get a larger reader, the 6 inch will still be the one that I carry around with me, and I'm pretty sure that I'll still use it to read journal articles / textbooks.
I hope I didn't make it harder for you to decide... if you can hold out a bit, I'm pretty sure that you will find a more affordable, larger reader on the market in 6 months or so. Pocketbook announced that it will be coming up with a 9.7 inch reader next year, that might be worth checking out as well.
If you are concerned about how a particular article will reflow on a 6 inch device, you can attach it on here and I can try it out on my reader, and hopefully put up some pictures if you like.