respect the missiles, but do NOT fear them.
You beat the missiles with most of your moves, when timed and spaced right. The basic defense is jab, or possibly tilted forward tilt. This of course is only as long as samus is not right in your face.
I mainly try to stay very close to samus, and throw out a move that will either hit her or force her to retreat. If she attacks with a missile, the attack will go through it and still hit her.
If she manages to get far away from you and starts to spam missiles, make sure you keep to the ground and shield (only if she's too far to grab you or otherwise punish) or jab/tilt them while slowly making your way to her. If you have platforms available, I find wavelanding on them to fast-fall up-air (to destroy any missiles) works pretty well.
If you're good at powershielding, that works pretty well, but be careful when she's right up in your face unless you're very consistent.
Also, be very careful when you're close to samus, she's in the air, and she's not lagging from something. It's very easy to get hit by a close range missle unawares. Make sure you have a hitbox out or are about to have one to intercept it.
when you're recovering, be aware that you can use a uair/fair to intercept any missiles she shoots at you. Don't rely on down-air to do the job, it has awful priority.
I haven't even mentioned the charge shot, since it's not really that much of a threat, I find. Just be aware how much charge she has, and be careful not to put yourself in a laggy position such as a mid-air dodge or side-step while she is not. For example, do _not_ sidestep a shprt=range jump-canceled missile she shoots at you, since might be following it up with the charge shot to catch you as the side-step's invincibility expires. (power)-shield/ (single-jump)/jab instead if possible. Also, just be aware that she can shoot the charge-shot pretty quickly while she's just falling. Don't be caught unawares whiles she's drifting down while recovering, for example.
Other than projectiles, be wary of the nair, as it comes out really fast and has great reach and priority. Try to bait it out and punish, since it has a fair bit of windup lag. Something like jumping and then falling instead of double-jumping at a falling samus, causing her to whiff the nair, and then punishing with a uair or fair.
abuse the fair and uair against her. up air especially is REALLY good against her, same as falcon's. You can juggle her for a few hits if you get one off usually. I get a lot of damage out of spacing bairs against them, it's hard for them to punish when spaced well.
samuses love to side-step down-smash, so try to predict and and punish with a down-air after the side-step, followed by more down-airs or fair-->uair.
learn to di the down-smash so that you can recover, it's wonky sometimes and can get you killed at low percents.
the tipman spike is really good for edge-guarding them, you can do it even if they sweet-spot if you do it right, i think. Don't be afraid to go deep for a reverse-uair edgeguard when you read a far-grapple, but try to space it so you can still land on the edge with your up-b (although this is hard in practice, it limits you greatly to be safe). I find that invincible ledgehop-uair can be a good starting point for a tipman edgeguard or simple backair if they panic-upb.
Also, you should never be getting shield-grabbed. When l-canceled and spaced properly, you should always have frame advantage against her shield or side-step enough to roll away, jab, or side-step. Again, Make sure you don't shield short-range jump-canceled missiles unless you're confident you can get a powershield and react, as that's another common way they get grabs. I will stress this point: Her grab is SLOW. Take that into account when, for example, side-stepping. Usually it's better to intterupt it with a jab or to roll/jump away. Be aware that the extender-homing grab cannot grab you in midair. The best way to avoid it is to simply jump at her and aerial to interrupt it. Don't try to sidestep as it will just wait for you.
well then, I've rambled on quite long enough...
