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It really depend on what you are going to use it for. For reading papers, textbooks, etc(specially if they have illustrations, equations etc and in pdf format) the EE is just better since you may be able to see the whole page at once. The problem is that it is more bulky and heavy.
I still find my self using the EE whenever I want to do some serious reading of mathematical documents. Having two screen is just great to be able to see two different pages at the same time or do a derivation in the journal while having the pdf in the other screen.
The PE is better if you are going to read epubs, or text only documents since the screen size doesn't matter. The PE is a lot lighter. Unfortunately, there are not that many technical textbooks or article in epub format. And even if they were, epub does not store annotations (annotations are stored in a separate database) so the functionality is not as good as pdf. I just prefer to keep the annotations together with the original document so that I can see them in other devices (e.g., in a PC).
I agree with Filark that the galaxy note seems like a great replacement for the PE. We'll see if AT&T brings it and at what price...
As for the EE so far I haven't seen any replacements. There are just no new double screen devices out there. And even worst there are still no pdf readers in android that are able to split the screen and show 2 pages at the same time or the pdf and another app to take notes. I guess the best replacement for the EE would be a windows tablet. Perhaps something like the Fujitsu Q550.
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