okay okay okay, let's calm down here.
upthrow to upairs is really good. samus is basically useless in the air, so keep your upairs shorthopped and sweet so that she can't juke you with a bomb and then she lands, negating your advantage. it's the same thing marths do to her. keep her airborne.
there aren't many set-ups for knees against her except a blind read or a nair to knee around 70-80. it may not kill but you can set up for an edgeguard easily
try to avoid nairing a lot in this MU. it is so easily CC'd and worked with. wait until higher percents for that, mentioned above. try and get a couple backairs, or a grab, or stomp > grab and get her in the air, working up some % with upairs. it's a solid strat. at 0%, you can upthrow, upair, regrab. get her back up there; keep her above you
i used to feel afraid to go out there and interrupt her bomb recovery, fearing i'd lose my stock with a poor dj into another bomb, but you should try it. just interrupting one bomb cripples her recovery
there's also a downthrow to knee but it's sort of a mixup. like, if they DI it right, you can catch the dj and knee with a full hop. if they catch on to that or don't fall for it, try to sh the next one. it's not guaranteed so don't rely on it
those are my thoughts on the MU i hope it helps