I read on my iPad everyday (manga scans) and don't notice the glare while I am reading. I set the brightness as low as possible, turned auto brightness off, and within the reading app I've lowered the brightness a little further. I didn't do that for glare issues though... I just did it because the iPad screen is really bright. The only time I notice that the screen has a glare is during a dark movie or when the iPad is off (at which point it becomes a mirror).
Maybe give the in-store iPad a second try. I don't think there is a better technical pdf reader currently available. I have a Kindle DX and as gorgeous as the screen is, it can't touch the pdf features of the iPad.
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