Thought I'd give my views on the legendaryness and creation.
When exactly was Mew called a God of any description, anywere, ever? It is the stated to be the "root of all pokemon", meaning that it was the initial breed of pokemon, not a God.
Red/Blue
So rare that it is still said to be a mirage by many experts. Only a few people have seen it worldwide.
Yellow
When viewed through a microscope, this Pokémon's short, fine, delicate hair can be seen.
Stadium
A mythical Pokémon of South America. A growing number of people have seen it recently.
Gold
Apparently, it appears only to those people who are pure of heart and have a strong desire to see it.
Silver
Its DNA is said to contain the genetic codes of all Pokémon, so it can use all kinds of techniques.
Crystal
Because it can learn any move, some people began research to see if it is the ancestor of all Pokémon.
Stadium 2
Apparently, it appears only to those people who are pure of heart and have a strong desire to see it.
Ruby
Mew is said to possess the genetic composition of all Pokémon. It is capable of making itself invisible at will, so it entirely avoids notice even if it approaches people.
Sapphire
Mew is said to possess the genetic composition of all Pokémon. It is capable of making itself invisible at will, so it entirely avoids notice even if it approaches people.
Emerald
A Mew is said to possess the genes of all Pokémon. It is capable of making itself invisible at will, so it entirely avoids notice even if it approaches people.
FireRed
A Pokémon of South America that was thought to have been extinct. It is very intelligent and learns any move.
LeafGreen
So rare that it is still said to be a mirage by many experts. Only a few people have seen it worldwide.
Diamond
Because it can use all kinds of moves, many scientists believe Mew to be the ancestor of Pokémon.
Pearl
Many scholars regard it as the ancestor of Pokémon since it can use all known moves.
All Canon, none stating it is a God. Just the root species. I remember reading that in one of the various Pokemon manga series it is said that all pokemon are of the one species, just different offshoots due to area, climate and living conditions. Considering the SciFiness of Pokemon G1, the Pokedex readings of Mew, especialy in Gen4, this would prove to be correct. While Mew does not evolve, and certainly not any type of diety, it would adapt to it's surroundings, becoming different species.
From this, I go to the infernal mindboggler that is Arceus.
Diamond
It is described in mythology as the Pokémon that shaped the universe with its 1000 arms.
Pearl
It is told in mythology that this Pokémon was born before the universe even existed.
While it is easy to see into it "Shaped the Universe" there is one key difference to Mew. Wording. Mythology is not always fact. Scholary involves research, and consider, while it is obvious the pokemon world was a very myth based place, it is now a very technological based place, so the research may have scientific basis, reason for wording aswell. I would assume the book that is ingame is a collection of Myths, not a research on their factual basis, again, due to no wording to assume otherwise. Likewise, with Palkia and Dialga, in canon(Games) we have yet to see Palkia and Dialga distort time, while both have the power to alter space(Thier emergance suggests they both have spacial altering abilities.) Dialga's pokedex does state, not "Myth Mention" it's time controling abilities.
This Myth talk also goes for the Hoenn Trio aswell. We see that Kyogre can create a rainstorm, on the level of Raindance, not on the level of flooding. Likewise with Groudon, he can intensify the suns rays like Sunnyday, nothing is done with land formation. Thankfully, other than living in extremely high altitude, Rayquaza has no "Godly" attributes associated with it in myths. These are obviously very gifted and powerful monsters, but far from land/sea creators. While I do not feel like copying it again, look them up in Bulbapedia, they state the words Myth and Mythology alot. As does Regigas. I'd assume the Regis, being human made, are based off of him, as he is "Legendary", the Pokedex states the word "Legend" in it's description.
Now, as for all this Sea Lord speak.
Kyogre is explained. He is credited with it's creation, but due to ingame events, lacks the power, he can just make it rain a hell of a lot. He dwells there though.
Lugia, on the other hand, while it does have alot of "It is said", but also has confirmation of it's extreme power from RSE, to the point where a light flutter blows down a house. All of this "Guardian" speak falls into the catagory of "Mythology, Legends and other non-factual Pokedex readings" Again, dwells in islands in the sea.
Manaphy, other than the Anime, with all it's pokedex, size, location, personality, ect descrepencies allocate Manaphy any greatness. Canon wise, he is nothing but extremely rare, like the Lati@s.
So, realy, we have no Ruler of the Sea, all are area legends. Closest is Lugia, as his power is shown to be so great, with Kyogre as a second and Manaphy as a nothing.
Darkrai's sleep lulling and Dream creating is confirmed, while the nightmares are folktales, which is a new term. :P While the Boy on Iron Island may confirm it's Freddy Krueger-ness, it is not completely confirmed. Likely, but not a definite yes.
Cresselia, oddly enough, has no power, status or any mention.
Ho-Oh's qualities are all Myths and It is said aswell, nothing grounded, quite odd is it's lack of mentioning power, considering Lugia's. Not even the Reserrection tale gets a factual mention.
The original two trios are interesting though,
Articuno's has no Myth Mention of it's ability to create a blizzard(Doubtful if they mean a battle Blizzard, it's be a pointless mention)
Zapdos's GenIV dex confirms it's ability to contol Thunder(same as Articuno)
and Moltres' GenIII confirms it's fire controling abilities.(same as Previous)
Entei has never had his eruption abilities Myth Mentioned, always fact, but with that said, we hear Entei Roar, not bark, and their are few Volcanos.
Raikou has never had it's thunderbolts and rainclouds disputed(With this said, it's bloody lame as alot of other pokes can use Thunderbolt)
Suicune is the same with it's purification capabilities.
With these six Legendaries, and these specific qualities, nothing is disputed, everything is stated as fact, no Myth, Legend, no "It is said", this is quite odd considering the rest mostly are. One can gather these have had enough human contact.
On the topic of Jirachi, it has never been confirmed, it is all It has been said in relation to it's wish granting powers, and I would not take the attack Wish as evidence though, it is learnt by many.
The last one I can think of that has been allocated a high spot is Giratina, other than it's high states and Grave Living, it also has nothing concrete.
For future refernce, I'd say, before believing anything, read the wording, then decide. Key terms
MYTH
LEGEND
IT IS SAID
FOLKLORE
Now that was a long post :P