Okay... Giratina is Antimatter. Let me rephrase that... He IS Antimatter. Antimatter destroys things quite effectively just by being there.
Dialga can completely control time. Literally. He can erase things from time or make something age ludicrously fast (or backwards). Or maybe change a little detail in history to put the world through Apocalypse.
Palkia has a move that's LITERALLY called Spacial Rend. He can rip things apart using FREAKING SPACE! He can eradicate the world. Space is kinda much bigger than our little planet.
To top it all off, Arceus can create all three. Easily. I highly doubt Arceus can create something with abilities that he doesn't have himself.
I always wonder why they are typed as such for the reasons you stated. What does palkia have to do with water? what does dialga have to do with steel? ( i could let the steel one pass though kinda ) And Giratina is a ghost.. that may have been explained though, i did not play platinum.
As for arceus. I question if hes even at full power when caught. He can change his type by carrying a plate. One would think when he created the universe he had all the types and the plates are remanent pieces of a more perfect form. Or perhaps creating the other 3 weakened him.
In D/P Cyrus states that catching Dialga/Palkia with Pokeballs severely limits their powers, hence using the RED Chain. so your first theory is most likely.
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If we want to take Anime/Movie accounts of putting these pokedex entries to the test...
--Gyarados nearly rampaged and destroyed the surrounding region 2-3 times in the anime.
--EVERYONE runs from ONE Ursaring.
--Haxorus controlled by Team Plasma (Bringing out it's full power) nearly destroyed an entire city. So much so, that Officer Jenny evacuated the citizens and put a traffic block.
--Iris' Dragonite, when wild, was so powerful that the police brought in the toughest trainers around after it practically destroyed the powerplant to try and recover. It was injured at this time.
--Mew Two, Dialga, Palkia, and Darkrai nearly destroyed the world in their respective movies. Oh, and Unowns created a fake Entei with enough power to attempt to perma-crystallize the world.
--Groudon + Jirachi = lolworldsend
Technically Palkia and Dialga did not almost destroy the world. They almost destroyed a single town...that was transported into a pocket dimension made by Palkia alone. Did I mention the Palkia was heavily injured and otherwise weakened at the time?
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