The lore in Diamond and Pearl suggest that Arceus first created Palkia and Dialga to regulate time and expand space. Then, creating Azelf, Mesprit, and Uxie who created matter. Then Arceus went into a deep sleep.
From there it doesn't explain more, use your imagination. I think the whole "ancestor" thing applies only to non legendary pokemon.
Then again every time they mentioned the ancestor thing with Mew they'd always have "BELIEVED to be the ancestor" rather than "Mew is the ancestor". It could just have been an analyst that some scientist made from random evidence such as bone structure, it's impressive movepool, ect. Just like how cigarettes were believed to be perfectly harmless in the early 1900's.
However it goes, I'm sure everything can be properly linked if the writers actually connected their stray stories.
So far we've got this (off the top of my head)
Arseus = God = First pokemon ever; Creates Uxie, Mesprit, Azelf, Dialga, Palkia
Palkia; Expands space