this match comes down to 100-0 because of one simple reason, if first shot kills, you've got 2 questions.
1. Who shoots first?
2. Does the second person get to shoot before he/she/it/potato dies?
For the first question, mewtwo's actions are simply FASTER, as I proved, he doesn't need to move to act, and finding samus is immediate and automatic. Samus need to find mewtwo and make physical actions (aka, aiming and firing). By the time that's happened, mewtwo has already executed his gambit and it's too late for samus.
For the second question, the answer is no. Since the result of mewtwo's action has no delay, samus doesn't get a chance to shoot back, so no mutual destruction.
However, it's not quite "first shot wins", it's first HIT wins. Since I've been ignoring them recently, here's mewtwo's options.
Also, the situation is first shot that hits, remember that. Mewtwo may not have the physical composition to resist, but he certainly has the options, and every beam that samus has is limited in what in can travel through (or it doesn't home), but only in the most pro-samus field is there not gonna be something mewtwo can use to block. For the 2D metriod weapons which can literally go through anything, they can't home, so hyper-compression (not necessarily a mico-black hole, just enough gravity to bend the path slightly) will through it off just enough to disrupt sniping.
As for actually attacking, mewtwo can use telepathy (samus may be resistant, but if she was immune, then how could mother brain hurt her with that telepathic beam, and space pirate technology would be only sufficient to screen, not eliminate) to puddle the brain or create illusions.
Also, the suit has shown vulnerability to being surgically removed in fusion (which mewtwo can imitate).
This is all assuming that samus' resistance really means anything (aka, the suit can stand the direct pressure, her mind can put up significant resistance). Mewtwo's power is canonically on par with dialga and palkia, you know, the guys that almost destroyed the world BY ACCIDENT in the latest pokemon generation. This suggests that mewtwo's powers are similarly apocalyptic level, in which case, samus' mind and suit would be akin to a toothpick to mewtwo.
Overall, mewtwo's options come out faster and eliminate samus' options once they come out, that's why mewtwo wins.