Hitstun makes knee comboing and combos into knee extremely difficult. It's more of a trump attack than a reliable finisher in this game. For finishes, Falcon typically must depend on bairs and uairs (edgeguarded, it doesn't really clear enemies off the stage but it's a good edgeguard).
The knee is much more difficult to hit in this game. The timing's different, and once you get it down it's easy to land on a standing target. Sure. You won't be able to get it constantly in a game though. That's a fact.
Also, the knee has to be executed later in most cases because of the sweetspot positioning, shorthop height, and opening time. This gives the target even more time to recover from hitstun. You have to be right up in there face to get it, pretty much, so that makes comboing into it a nightmare. I've managed to get it to work into combos against players who have mid-priority moves that utiilize the full body to attack though (Pikachu, Diddy, Kirby, but not Puff, puff is ridiculous).