Why is NYTimes.com inferior to The New York Times? I mean, other than the aforementioned lost serendipity? The story that is put to bed for the hard copy in the middle of the night is updated to within an hour or two when I get it on the web.
Just because it's electronic doesn't make it inferior. My choice of reading matter is the same. It's the medium that changes. In this case, does McLuhan still hold?
As far as the individual stories are concerned, you're right to note that the electronic version of an article is often updated or modified after it's first posted, and this can be a good thing.
What I think most online versions of print publications have a difficult time with is conveying the totality of the issue. When I look at my local papers (we have two dailies in Seattle, and my household gets them both) I scan the front pages of the sections and then read the stories I'm interested in. The layout of the page tells me a great deal about which stories are considered important, or connected -- over time we've all learned to decipher the semiotics of a newspaper page.
Very often now, though, the individual stories in the electronic version are displayed just like that -- individually. The screen doesn't always tell you which was the lead story, or which was a related piece. In some cases, depending on the way the site is programmed, you can wind up looking at material from several days ago without knowing it, by clicking on a "more" button. Jusst thinking in terms of dance coverage, you don't necessarily get a "picture" of the dance community on any given day, but instead a series of related pieces that may or may not comprise the entireity of the dance writing that day.
Of course this is all leading to podcasting, where you pre-select the topics you're interested in and the seach engine takes out all the bits it thinks you don't want. This assumes that there is very little that is expected to engage everyone -- the myth of the general reader seems to be imploding even as I write. And yes, there are whole sections of the paper that I never look at (sports goes into the recycling pretty much just as it entered the house, unless I drop it accidentally and scatter it around), but I do think there's something valuable just in knowing it exists, even if I choose not to explore it.
Some papers go out of their way to replicate some aspects of their print version (up to and including pdf files of their pages) on their websites, but I still see more of the floating articles (geographically unanchored).
To answer the last part of your question, I think McLuhan is even more accurate now than he was when he was first writing -- with the Internet and its attendant developments, the medium is very much the message.