It's more a matter of the current model of the Reader not being aimed at 'serious' readers, in the sense of researchers or those studying a text. It's intended as a device for
just reading books, leisure reading, if you will, which it does rather well, in my opinion.
I agree that there is a definite need for a more serious, work-oriented device. Something with an A4 display, pen input, and a more powerful application set that allowed things like annotation and searching (among others) would be a huge boon to any number of professional pursuits: academic (students and teachers), legal, medical, research, news media, and office environments of all sorts would be able to make great use of such a device.
However, the Sony Reader (this model, anyway) isn't that device, wasn't ever meant to be that device, and never will be that device -- it would require too different a hardware set to get there.
But, it's not the only device out there, and I somehow doubt it'll be the last one Sony makes, for that matter, however soon or not they get around to doing so.