I haven't played many Metroid games, so I was just wondering.
It's mostly due to how Samus compounds all of her powers, never really replacing any old ones, but making the sum of her abilities even higher. Each new beam
usually just ends up becoming part of a bigger beam unless it specifically conflicts with another beam on the stack. So now any new conditions (Like freezing for ice, hitting multiple enemies with plasma, etc.) are added on plus a damage multiplier for each one.
So her beam is super strong. Then take into consideration that she can collect about 12 of those energy tanks in Super Metroid. That's 1200 life + the base 99. If the OP allows it, it wouldn't be hard to say that she can have all of the energy tanks from every game because it was never explained why in between games that she lost everything. So, technically, she has access to ever upgrade on every planet because hers is one big flowing universe unlike the Zelda or Mario universes (for example) that aren't as continuous and a bit more problimatic to carry stuff over from.
Lastly, the Power Suit is able to handle so many different kinds of situations. The Varia suit stops her from being hurt from extreme temperatures, frozen, and acid. The Gravity suit allows her to move freely in water and not be hurt by lava (Super Metroid, not Prime). The Phazon suit stops radioactive damage. The Light suit stops dark-based damage. And I'm sure I'm missing more. And, much like with the weapons, for each suit she had on there was a bonus to damage reduction. And, since nearly every game doesn't explain why she loses the suits between games, it would be logical to say she has access to all of them.
Not to mention all of the badass things she has like the grapple beam, speed booster, space jump, screw attack, etc. The visors are also pretty nifty for certain situations...
So, yeah, Samus is kinda broken. The only thing that I've seen that can stop her is Ganon, because he has hacks. Seriously, nothing can hurt him aside from weapons in Link's universe. So, until Samus can parallel dimension hop, then she can't beat Ganon as well as any other non-Zelda character.
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For my last note, Samus should be over Sonic. Sonic really doesn't have a projectile move, and Samus does. If she hits him and he has no rings, she wins. If he goes Super Sonic, she can just continuously screw attack using the space jump OR speed boost until he runs out. Then, it's just a simple matter of hitting him 1 time with anything she has... and she has a lot.