OK now, here's my first theory suggested, but covers all the legends:
In the beginning, there was nothingness (if it's even a word). Then, out of chaos came Arceus. He created 3 disciples, Dialga, Palkia, and Giratina. Each of them were supposed to have a job each. Dialga and Palkia did their jobs of creating time and space respectively. However, Giratina did not want to help Arceus and instead, he rebelled. Hence, Arceus banished him to the underworld where he would become a devil. Then, soon after time and space were created, Dialga and Palkia lost control and started pandemonium. Arceus created the Powerpuff Girls (Mesprit, Uxie and Azelf) to quell the two. Dialga and Palkia were sent into a different dimension whuch was controlled by the PPGs.
Then, Arceus created Groudon and Kyogre on a ball of matter. These two would eventually shape the ball of matter into a planet. Then, the two could not get along and started fighting, most likely for territory. Arceus saw this and created two orbs, which quelled them and put them into a great slumber. Rayquaza was then created to create the skies and guard the Earth from internal and external threats.
After creating the skies, Rayquaza decided to regenerate his energy by slumbering. He created Ho-oh, who would guard the skies, and Lugia, who would guard the seas. Lugia and Ho-oh, created their own disciples. Lugia also created Manaphy, who would be the second guardian, thus explaining the "prince" title. Manaphy then had a son, Phione, who would be the third guardian. Then, Arceus created Regigigas, who towed the continents that Groudon created together. Regigigas then created his own disciples to help him fertilise the land with steel, rock, and ice. Regigigas then fell into a petrified state after draining his energy.
Then, Arceus created Mew and Shaymin, who would represent Pokemon and plants respectively. Pokemon decended from Mew while plants decended from Shaymin. Creating these took a lot of energy, especially Mew. Arceus gave up his power to learn all moves and gave it to Mew. Then, Arceus decided to regenerate in the Hall of Origin. This would leave him in the state he is now.
Shaymin flourished the land with flowers and created Celebi to guard them. He gave Celebi time travelling abilities, allowing him to guard ore effeciently. Mew gave birth to a lot of children, which are the Pokemon we see now. Mew also created humans, who would get along well with Pokemon. Darkrai and Cresselia were born from the dreams of people and Pokemon. Jirachi was born out of their wishes. Unknown to Mew, one Pokemon escaped from Earth and went to live in space. That Pokemon is Deoxys.
For Latios + Latias:
They are rare Pokemon and are said to be legendary because they can control waves.
Heatran:
Rare and last few of its kind. Cannot breed with Ditto because it lived so long ago that Ditto couldn't recognise its genetic structure.