It's a pretty well-known fact that only holy attacks can defeat Ganondorf, but Samus doesn't use any.
In Metroid Prime 2: Echoes, Samus uses the light beam, which is effective at killing the Ing, Warrior Ing are the most common and the description about them are as follows:
"Morphology: Warrior Ing. The soldiers of the Ing Horde. Shapeshifting wallcrawler. Dangerous combatant in melee and at range. Dislikes bright light.
Warrior Ing are challenging foes. They can render themselves into amorphous puddles and move over most terrain, including walls. Warrior Ings can turn their bodies into dangerous projectiles sheathed in dark energy. The tips of their legs are razor sharp, making them formidable in melee. Finally, Warrior Ing are capable of channelling transdimensional energy and firing it at their enemies. Their only real weakness is bright, pure light, which they hate and fear."
So Samus does use one, at least. However, this "fact" is only true in the Zeldaverse, which is to say the people in that universe are only aware of one or few weakness against Ganondorf. They are also claims not made by any omniscient being, but by people who are aware of the most effective way of killing Ganondorf. It would be like me living during the times where there was a mass hysteria of vampires and I said the only way to kill a vampire was driving a stake through his heart. It wouldn't mean that's the only way vampires can die.
Tell me how Ganondorf would be able to withstand being frozen by the ice beam and then being shattered with a concussive blast. This is how Samus thinks. To support this claim, I'll quote from the official Metroid Prime Web site, which says:
"One of Samus' favorite tactics is to freeze an enemy and then shatter its body with a Missile [sic] attack."
Proof of Mewtwo's TK strength, also him crushing.
The first one is pretty cool, but what are Poké balls made of and how much pressure can they withstand? The structure appears rather thin, which would make the object weaker to forces and pressure. A can made of aluminum, for example, can be crushed just by stepping on it. If the can was in the same form as a can, but it was entirely solid, it wouldn't be so easy to crush by stepping on it. In the games and manga, it's destroyed if a wild Pokémon gets free from capture.
And while this is all great, these are the anime, not the games themselves, which take precedence as they are the primary source. Maybe if you could show me from one of the games, that'd be nice. But let's say we accepted what's going on in the anime, Samus has withstood gravity, which I have calculated to be 7.88 times greater than Earth's. Her jumping is reduced, but she's still able to wall-jump and run just fine under these conditions. The gravity feature nullifies these effects.
Under 7.88 g, Samus would weigh 1,560.24 lb., which is a little over half a ton (0.78 tons) This would mean her organs would experiencing this as well, but let's forget about that. With the speed booster allowing Samus to travel "supersonic speeds", the moment she shinesparks, she would experience an acceleration of 70 g. Just think about a human being in those conditions. Not only that, Samus has to come to a complete stop, and yet she walks (or runs) as if it were nothing.
Please read:
http://en.wikipedia.org/wiki/John_Stapp#Works_on_effects_of_deceleration
Now tell me how Mewtwo would defeat Samus.
Do you even know what a goddess is?
A feminine title for "god". Being a god or goddess doesn't mean anything. Only feats matter, otherwise, I should care what has to be said about Palutena.
We saw DK knock down the moon, and Mac has around equal strength to him. Maybe DK wasn't using full force, but Mac is still stronger physically.
Yes, a moon magnitudes smaller than our own. Punch Out!! was released in 2009 for the Wii, where as Donkey Kong Country Returns was released in 2010. You're trying to work backwards here, which isn't how this works.
Unless Samus' suit has moon-level durability (and I'm guessing it doesn't), Kirby could blast it open using the Star Rod and kill Samus.
Prove that the Star Rod can destroy moons.
Meta Knight didn't defeat Marx, but he defeated the strongest in the galaxy, making him pretty tough.
The toughest in his galaxy.
Well, there's nothing saying Sakurai wrote the Kirby trophies (particularly in English), is there?
Of course not, but being creator of the series, I'd expect he has more say in the matter. With that mentality, we should ignore anything written by anyone other than one who wrote it, especially the translator. That would be a lot of information thrown out. Would you then suppose Kirby is larger than 8 inches?