I doubt Samus would OHKO ALL Pokemon, especially the legendaries. I think if not for the actual Pokemon Trainer himself, the Pokemon would win. Using Mimic on the Phazon Beam, Speed Booster or whatever would prove very useful. Spore and Thunder Wave also would put Samus at a disadvantage.
I kinda doubt pokemon could mimic phazon beam, as phazon beam needs internal phazon source for it to work. And besides, corrupted samus GAINS HEALTH from phazon, not lose it. xD Pokemon would also doom themselves when coming in contact with phazon when trying to fire a phazon beam lol.
In any case, I also doubt mimic could work against any of her weaponry, because what you need to produce those is a chozo suit. Pokemon moves come from the pokemon themselves (like producing water and flames from mouth, aka empty space), they do not need extra things to produce attacks whatsoever but use some sorta internal energy to produce those attacks. (I imagine the amount of internal energy needed to produce an attack of different force and effect transfers to PP, usually the stronger the attack, the less PP you have). Mimic cannot copy Shadow moves for example, because non-shadow pokemon is unable to produce such attacks and mimic instead states "but it failed!" when you try to copy shadow move as your last attack. Mimic also fails when used against protect, so her invulnerability would render a mimic pokemon unable to copy her last attack move.
Samus has also shown immunity to poison effects, alongside phazon radiation and Dark Aether climate, though she can still take damage from venom weed and acid because they strain her suit's force field protection, if you're in contact with poisonous substance for extended period of time. She's protected inside her suit, so no actual ailment moves that do no damage would effect her. She cannot get status ailmented per se, unless it's a computer virus or an electric attack, but in that case her suit basically reboots itself if it's a virus and the paralysis from electric attacks only renders her HUD inactive for a moment. T-wave can miss however and she's invincible while in her hyper mode, screw attacking or speed boosting.
Samus would only need to ohko in case of someone using mirror coat, but the only notable mirror coat users that could actually take 1 charged beam shot before getting pwned would be wobba, deoxys defence forme, suicune, tentacruel & swampert. But Samus is not limited to one beam shot in any case and can rapidly fire many super effective beam shots, alongside using moves that incinerate targets such as power bomb.
Lucario is half steel, so any liberal use of her plasma beam would deal massive damage to any Lucario. >_> Not only that, but the plasma beam would also go through that pokemon and hit Red/another pokemon as well. <_<; I'd ill advice against using steel types cept Heatran, simply cause her plasma beam has fairly quick rate of firing things.
In any case, PT can have 1 pokemon out in the beginning and then needs to toss out all the rest, but Samus doesn't even need to deal with the pokemon and can just go for PT himself. She has many things she can use to just wipe PT out in one move. It only takes 2 seconds to lift her arm cannon and fire imperialist at PT, or 3 seconds to morph, boost the distance and drop a power bomb at his feet, 4-5 seconds to go into hyper mode, lift her arm cannon, charge phazon beam and let it roll etc.
Oh and what about that Omega Cannon she can use in Hunters? That nuclear weapon of mass destruction?