Except containing samus would be a casual act, not something to cause fatigue. Hold her aloft, keep her gun pointed at herself, apply some redirecting force to keep her from moving to anything she can use (that way he doesn't need to oppose it).
In the meantime, mewtwo can just carry on with his life. You know, eat, drink, be merry.
I will also note that stone blocks in mechanisms have shown capacity to do damage and even crush samus in her morph ball form.
So, mewtwo could put stuff above her, heavy enough in total to destroy her, and let gravity do the work.
The scenarios are bunk.
But again, so far I've only touched on a tiny bit of mewtwo's ability.
I wanted to establish that mewtwo has at least one perfectly viable, inescapable scenario. And again, mewtwo will shoot first.
From there I can start dismanteling arguments that mewtwo's telepathy can't puddle samus' brain, that mewtwo doesn't have the raw power to crush her, ect.
I'm concentrating on this because it got lost in the shuffle.
For the ship to transfer useful knowledge, it has to be nearby.
Ultimately the issue comes down to you're making assumptions about what happens before they are put into the battlefield, but we're essentially dropping them there.
Basically, if we make assumptions like that, we get into issues of who anticipates farther ahead, and then we get a situation like this:
http://www.youtube.com/watch?v=NZktNoK4wDo
2:44 onward.
Finally, let me point this out, even if she knows where mewtwo is, she still has to physically aim, lock on, and fire. Mewtwo only has to think, which is faster?
As for the vizor, in the picture I showed, those solid walls completely eliminate the effects of the vizor. So, the point is, it depends on the material, it can't penetrate everything.
Again, remember, they're x-rays. X-rays don't go through everything.
If nothing else, using the scope from longer rangers clause the things that you can actually see to build up, making a picture impossible.
Hyper beam has functionality, but it's not the actual beams.
That's the point I was making, it's a unique weapon regardless of it's functionality.
EVERYTHING creates it's own gravity field.
But only extremely powerful gravity fields can counteract the effects of a black hole. You know, like another black hole, and it has to be outside to pull things away from the black hole. Putting a tiny slide on a large slide doesn't mean that it won't slide down.
Do I really have to explain basic physics behind gravity?
It's not about the weakness, it's the fact that mewtwo in smash is not actually mewtwo, it's just a trophy that looks like mewtwo.
It's created to be similar to actual mewtwo, but it's not really mewtwo.
Thoughts are faster then actions, thoughts have to occur before actions can.
Samus has to find and lock onto mewtwo before she can fire (if she doesn't lock on, it'll home in on random fauna). Mewtwo will know where samus is immediately.
Mewtwo shoots first.