It's sounds like the missiles are giving you the most trouble. Assuming you're playing a regular Samus, I'm assuming there to be some crouch-cancelling d-smashing involved and up-B'ing out of shield as well. I hope these are valid assumptions. ^_^
When I'm playing a Samus, it's expected that there will be missiles, so it's necessary to close the distance quickly. If the missiles start firing before you're close, then it's time for "missile command" as I call it, and you're going to have to time your full-hopping (sidestepping doesn't work if you have Nana) of the missiles so that you don't get hit and Nana doesn't either. Shield if you have too, but you're mainly trying to dodge them. A small tip might be that if Nana gets hit by a missile, shield maybe two, giving her time to get back on. Wavedash out of shield, shield a missile, wavedash out of shield again to get close may be helpful at times like this, however, Samus could simply firing two missiles in succession to discourage this.
Usually when Samus is doing the missile barrage, there's a certain length where she'll slow down the missiles and prepare to knock you away so she can start it up again. If you mess this part up, you'll be back where you started. When you're close to Samus, prepare for her crouch-cancel you (grab or d-smash), shield so they can up-B out of it (shield to bait out the up-B, grab, or space an attack well), or maybe just attack you (n-air or f-smash I think are most probable, with a wavedash there at some point). It all depends on the kind of Samus you're playing, and when you're close you're going to have to be one step ahead of her. This fight is possible, so have hope. ^_^