1: Legendary Pokémons
Most of the Legendary Pokémon are from Sinnoh. I find it logical, as Sinnoh's dragons created space and time. Arceus is the god creator of Pokémons so it is also logical to find so much Legendary Pokémons there. Sinnoh is an independant story, like for Unova. The difference is that the latter takes part much further than the rest of the regions, which are not far each from the other.
Pokémon Diamond and Pearl (and Platinum as well) could have a hidden
storyline involving Arceus, who created the Pokémons. I seriously do
not want to enter in religious facts, but Arceus bears resemblances
to God. He could've created Pokémons, and then see that humans
abuses them. So he had to create Legendary Pokémon to teach them
stuff and stuff:
1.1. Uxie, Mesprit and Azelf taught respectively knowledge, emotion and willpower to humans.
1.2. Cresselia and Darkrai are at the origins of Dreams and Nightmares.
1.3. Jirachi taught wishes to humans.
Dialga created time.
Palkia created space.
Giratina symbolizes the greedy human, who was banned for eternity.
Heatran is the creature of Volcanos, possibly the result of Groudon's Eruptions.
Humans created Regigigas as a Guardian.
6.0. Regigigas created itself three Pokémons:
6.1. Regirock, the Stone Age.
6.2. Regice, the Ice Age.
6.3. Registeel, the Iron Age.
Manaphy is the Cold Seas Pokémon.
7.1. Phione is the Warm Seas Pokémon, explaining how its "elder" Manaphy gave it its warm love. Like the Mother who gives to her Children love and warm.
Shaymin taught Gratitude to Pokémon, like how it is grateful to nice humans who gave it flowers.
Celebi is the time traveler, sent by Dialga probably to test the time...
2: Third Line Pokémons
This is no relations to Arceus. This is Game Freak's choice. Presumably, it was done not to leave some Pokémons weak; Magmar and Electabuzz, for example, were introduced in Gen1. But players found them weak over the time. Game Freak listened to them, and so created evolutions for them. But on the other hand, it can be considered lazy, because they took some old Pokémons and gave them evolutions.
I have something to add: Game Freak would've kept some Gen4 Pokémon unreleased, and release them in the future, like Gen5, because Gen5 Pokémons are ugly, and Gen6 introduced a little number of Digimons.
My mistake ... I mean Pokémons. (Wanted to sun funny ;)
Sorry for the long answer. Hope you like to read! And hope this helped! And merry christmas.