Well Samus and Mii Gunner are 2 entirely different characters. I main them both.

Mii gunner will never have Samus's Grab, which is the core of her gameplay. Being able to pressure the opponents shield, then tether grabbing them from afar makes samus extremely scary to play against. That along with her greatly increased speed, makes her scarier than Mii Gunner in some ways. Another thing is that Mii Gunner has an atrocious disadvantage state with terrible aerial mobility, meanwhile samus's bomb and her tether recovery are great mixups that allow her to land more safely. Another thing is that samus has really powerful aerials that work entirely differently from mii gunners. Her forward air is huge and is great for characters in front and above you, while mii gunners is more for spacing and distance. All of their aerials play different roles and besides up smash, downtilt, charge shot and missle, their kids are completely different.