that is a very melee-esque samus

try using your ice beam! at lower percents the regular beam is really good because it combos well and tacks on damage quickly, but with ice beam you can be killing him a lot faster.
dthrow-> fair or dthrow->usmash are fantastic on mewtwo.
Ice missiles do less percent, but they travel faster, which is nice.
A quick way to switch between beams is to taunt cancel, it's not terribly hard to do, so I suggest practicing it.
I notice you sometimes use upB for recovery, I find that, in most cases, it's a lot safer to just stick to airdodge to the stage or zair. Zair has about the same reach as your upB, and it always sweet spots. it's also very hard for people to edgeguard it.
with zair you can also cancel it once you start moving and then upB to mix things up.
Another point to help you adjust to the new samus is that her uair is an incredible combo move. you can also jump through your opponents shield with a uair and it is very safe on most characters.
some tips for the mewtwo matchup:
Always look for the teleport. mewtwo is looking for you to do something punishable and then he's going to teleport in with either nair or fair (usually)
If you can figure out the situations which he wants to get in (usually after you whiff an attack or get in the air) , you can punish him with a nair or a retreating shffl'd fair (Ice beam)
if he's going low to the ground, which he usually is, you can wavedash back into a grab or a tilt or smash.
mewtwos love to use confusion near the ledge or in neutral against samus (especially when they are at higher percent) to try and reflect a charge shot or missile (they throw it out a lot more when you have a fully charged shot), so try and bait the confusion out and punish it (you did a good job with that for the most part, I just saw a couple risky confusions I thought you could have punished)
That's about all I have.
Other than that, great samus play, you're still adjusting to the new features and the new matchups, but yeah.