Be of good cheer, skyscraper fans: it's a fair assumption that barring acts of war, economic collapse, natural disaster, or Singularity, most tall buildings will still be there. In a normally functioning capitalist economy a skyscraper is an artifact of very high land values; when buying a lot is expensive, you'll get more return on your investment by building high so there's more space to rent out when the structure is completed. (To be sure skyscrapers are also frequently an expression of human ego -- see Trump, Donald. But even Trump probably wouldn't build so many monuments to himself if they weren't going to make money.) However, it's generally accepted that beyond a certain size the ROI curve flattens out due to the increasing expense of constructing the building and the risk of glutting the rental market. Add to that the ferocious expense and danger of demolishing an already-present skyscraper in the middle of a crowded downtown and you are rarely going to see one tall building replaced with another.
Of course, any building in a skyscraper-choked downtown area that isn't a skyscraper is going to be at grave risk, because that's a valuable plot of land that could be easily improved. Unless the place is a bona-fide landmark with a mob of historians willing to park themselves in front of the bulldozers with arms linked, it's quite likely to be bought, demolished, and replaced with something huge. Thus the fate of the Sun-Times Building, now being replaced by the Trump International Hotel and Tower.
So my prediction would be that even after a relatively large length of time has passed cities that already make heavy use of skyscrapers existing downtown cores continue to look much like they do now, with a mere sprinkling of new structures, and newer and larger buildings rise at the edge of downtown instead. The real joker in the deck would be any new advances in materials science or some new type of construction technology that would make it possible to construct entirely new kinds of buildings.