I completely understand your reasoning. My main use for an eBook reader is to read "Project Gutenberg" out-of-copyright stuff, and the Sony is fantastic for that. It doesn't do a terribly good job of displaying "raw" text files, but literally a minute's "massaging" them in Word into an RTF file in a suitable font and they look great. It's not the "perfect machine" but it's pretty damned good at what it does
If pre-formatted PDF files are an issue for you then you're absolutely right, Reader wouldn't be a good choice. The best format for it is certainly RTF, which it handles very well indeed.
As I say it's not perfect, but I've been reading eBooks on various devices for probably the last 10 years, and this is the best machine yet for my needs. Things can only get better in the future.
Hope you find what you're looking for,