I would keep the damage on the charge shot. No need to nerf that. You should be rewarded for getting it off on someone, especially with a poor character. But yes, increase the knockback a bit.
DEFINITELY increase the knockback of the nair. Samus' really doesnt do well in the air when being rushed down by an opponent. a lot of her strengths come from a distance - charge shot, zair, missiles, etc. adding increase kb for nair makes it so she can knock enemies away to start her long range options, gives ok reward for a move that lasts sort of a long time, adds edgeguarding options that she lacks, and more. theres too many awesome uses a strong nair has, and samus is definitely a character we have to focus on buffing.
As for what The Cape was mentioning with the bomb drop I think this would work:
-Speed up the start animation (start till bomb) just a lil bit, not too much
-Decrease the cooldown lag a lot so she can do stuff after she drops a bomb
-Would it be possible to make bombs explode on contact like they did in Melee instead of being timed like in Brawl? This made them practically useless for on stage use.
Fsmash - incr kb a lil, not too much. samus has no good reliable ground horizontal kill options. while every character doesnt need an option for everything, fsmash is what it is. not the fastest attack that should be strong (like most smash attacks). samus has a hard time killing and this is a great thing to help change that.
Anything with making missiles better I immediately approve of
Will add more later, i havnt played Samus too much recently.