I fly to Europe from DCA, and the new version does not let me easily force the city in which I connect. A recent search offered one JFK connection (ok), two LGA-JFK (not ok) and a bunch of two stop possibilities (also not ok). Trying to force one stop in the cities I wanted (where I have changed in the last year) produced the error message listed above "You can't book connecting flights as individual flight segments...". But Google flights seems to find my routings and allows me to book on AA, so only a minor inconvenience.