The soundtrack is all wrong
The endless stream of "oldies" was distracting from the actual story, which was about two people meeting through the medium of (what was then) modern technology. While some of the songs were obviously picked for the relevancy of the lyrics, the overall effect was jarring. If the whole point of the movie is "the future is now, and tomorrow's relationships could look like this", why continuously remind the viewers of the 1950s/1960s?
Some will say, "Those songs are timeless urban classics", but they don't really have a place in a story about the modern world. The only possible explanation I can guess would be the nostalgia elicited by Shop Around the Corner, which we are told started in the 1950s. And yet the film's forward-facing agenda repeatedly reminds us that the old days are gone and are being replaced by something new. You've Got Mail would have been better served with a (mostly) synthesizer instrumental soundtrack.
If one wishes to see a "rom-com" that does the soundtrack right, watch 1990's Green Card.