The safest ways for me to combo and deal with this metal menace is avoiding the Nair first off and the Missles second. I prefer to Power shield and reflect them but I think the the Nair works fine, Nair>Pound>Nair or Bair usually lets you past a missle and a blast.
Safest way to rack up damage? I say Pounding and WoP. But if you can Grabs into a Dthrow and Bthrow or which ever is toward the edge is fine. I find that Fsmash is unexpected when they are getting to the ground if you are ever there. It out prioritizes Samus's Dair and Nair.
As far as killing Samus can stay close to you for the most part @like 50% with Fair and Bair. once its over like 70% start moving them to the edge. I find its easy because just getting hit by the bombs can ruin the chance of Samus recoverying. Also Stages Stages. FD even on my part, and I do love playing there, is a big no. Mute City and Battle Field are good choices along with Kirby's place.
So basically to sum, WoP and Pounding, Avoid Resting, Nairs and Pounds, Get in the way of bombs and WoP it off the stage.