Arceus does not directly create every legendary.
^ This chart might be of interest to you. But take it with a pinch of salt.
A few points about the chart:
1. Regigias was not created by man; Regigigas just existed (aka created by Arceus) and Regigigas in turn created the 3 golems. It was sealed away by humans who thought it was too powerful, and they also sealed away the 3 golems, who would be the 3 keys that open Regigigas' seal.
2. There is a theory about the Dogs trio; Suicune, Entei and Raikou. They were once Vaporeon, Flareon and Jolteon, the original Eeveelutions. Note that their typings are all the same, and the Dogs trio hidden abilities are the same as the Eeveelutions normal abilities. The Brass Tower (later Burnt Tower) was engulfed in a fire, and
three unnamed Pokémon perished in the fire; Ho-Oh returned briefly to revive them after the fire had been put out.
Legendary Pokemon can create other Legendary Pokemon; it's not just Arceus that can create.
3. It's not really known if Dialga created Celebi or Lati@s, but because Dialga is seen as the master of time, it makes sense that it created Celebi, which can travel through time, and the Eon Duo, who by their name are linked to time.
4. Same with Palkia; since it's the master of space (all space, including alien space), it makes sense that it was the one that created Deoxys, and indeed the Weather Trio who represent a portion of space on the Pokemon planet.
If you find something else in this chart that doesn't make sense... don't ask me, cause that's all I got. :I
Also, there's a huge speculation post here:
on tumblr about this chart & the origins of Pokemon.