Falcon would probably go even or win very the MU very slightly [unlikely he'd lose...?] without knee because he'd have no effective way to finish her off... but without uair he'd have a much less potent combo game on her [yay combo SDIing nairs].
Apparently HugS thought at some point in time that Samus won. Almost certainly not the case, but the Falcon MU isn't hot garbage at least.
Missiles lose to hitboxes and dair beats CC. Falcons that know to nair through missiles and good places to stomp will make things a lot more difficult.
so it's his combo game on samus and safer approaches that make the MU bad?
what does samus do to approach then?
Samus doesn't actually have to approach... her projectiles may lose to Falcon aerials when times well but she has projectiles and he doesn't.
That said, beyond hard reads (nair or fair to stuff an approach) she can probably try to poke at his dash dance with ftilt or maaaybe utilt/dash attack [Falcon's CC options that aren't grab are really mediocre] and missiles falling from platforms as mentioned above. If they do a bad nair or you intercept their DD a CC dsmash can set up an edgeguard situation [or dtilt can set up combos], but that's not likely as you play better opponents.
You could look up Duck vs S2J or something and see what he does, watching is probably a better answer than random advice.