How many websites have user-definable menu shortcuts, unlimited undo, instant user-feedback for every operation, tooltips that can be switched on or off, full internal drag & drop and OS-level drag and drop of files, standard user interface elements that work how the user expects them to work, a context-sensitive online help system, reconfigurable toolbars with user-definable icon sets, multiple open documents at once, movable and reconfigurable tool windows, manye internationalizations, and so on?
The web is still the future, I know, but web application UX designers are still re-inventing the wheel and without some enforced UI guidelines like Apple had in the 90s websites will never fully catch up with desktop apps in terms of usability.
To be fair, a comparison with modern desktop apps is much more favorable, because most of them have regressed in terms of usability.