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Points 2-5 unfortunately are far more difficult to achieve if my understanding on of how the ePub format works. ePub is, essentially, an electronic version of a book not dissimilar to a PDF file. While a PDF file is absolutely rigid and you can't adjust anything beyond the size at which the whole file is displayed an ePUB will let you adjust font and font size. The problem is that like a PDF the 'length' of the page is basically set in stone and does not adjust for the size of the screen you're reading on. So if the page length is set at 11" and you're reading on a 5" screen you're only going to see the page in 5" increments. This is demonstrated by the fact that I have come across pages while reading on my Nook that cut off mid-sentence within the top half of the screen and then pick up again with the rest of the sentence once I go to the next page. So, sadly, I think this is a flaw in the file format that might not have an easy fix. I could, of course, be wrong as I am not a programmer but that's how it appears to me.
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Then it's a serious flaw, not with the epub format, but with the program written to read them. Palm's eReader program designed for the PDB format can calculate precise page numbers, even when fonts are adjusted. The EB1100 also did this. The info for each font and page calculations were never discarded, but rather saved and then linked to the file in some manner such that deleting it from the device also deleted the information.
I shouldn't expect the Nook's firmware to fix this, because Adobe is the software designer responsible for it.