I haven't had the pleasure of playing a Samus matchup yet, so I can't spill the goodies on how it's done, but I also play Samus quite proficiently so here goes.
Your main obstacle will be the missile game. She's trying to use it to force you to hold still, so don't let it happen. You'll have a better time on stages with top platforms with low blast zones, like Yoshi's or Fountain of Dreams.
If she's short-hop missile-ing, simply take to a lower platform with a waveland, short hop from the far end, and throw a N-air that is spaced so that the second kick would just barely catch her with your thigh, going way passed her if you miss. This is because she has the option of back wavedashing and F-smashing you, but hopefully you're able to go far enough to where she would have to double wavedash, which she either doesn't have the room to do, or will attempt it and get grabbed. Remember she can begin to predict this and dash into Fire U-smash, but you can usually still dbl jump at the time she would want to be doing that, granting you a free dropping D-air or F-air.
Reserve the option to double jump out of your Short hop whenever possible, because Samus is kind of like a turret, and doesn't have any glaring blindspots while in place. The dbl jump will often bait an early U-smash or hop from her, and either of these will get her deliciously launched upward for combos (punish the hop by fastfalling then sprint to SHFFLd Up-air).
When she is charging B, don't assume you can just hit her out of it. Instead, try sprinting then shield. If she fires, it's blocked. If she stops charging in place, you can jump out of shield and reposition or try for some dropping aerials. If she rolls toward (usually out of panic), she will be grabbed. If she rolls back, you should Wavedash OoS and try to capitolize (don't attempt if you can't WD out of shield or if you simply didn't do it fast enough) with either grabs or D-airs, grabs being the quicker option.
A good Samus will often predict your shields against missiles and use this as an approach leading to sprinting grab. This is a simple game that actually benefits you. First, try jumping OoS and dropping an aerial. If she threw the grab, your next aerial is guaranteed, so make it count. If she retreated, make sure you don't try to come in out of expecting the grab, because you can still use your second jump to bait the U-Smash or hop or use it to retreat, landing on a platform or just getting away. Her final option most likely option for a lot of players if she saw the jump would be to wavedash back and go for missile games, which I've already covered a bit. The only option I see her taking besides these is jumping straight for you with F-air or N-air, both of which will lose to a dbl jump aerial on your end, usually knees
All I feel like typing right now, sorry.
Good luck, sir.
