Perhaps Anakin left Obi-wan after a period of training to become a full Jedi, like Luke did with Yoda. Everyone imagines the adventures of Anakin and Obi-wan, but it could be that Obi-wan fought in the first Clone War (whatever that is) and helped Bail Organa in that war, and then retired to train Jedi, like Yoda. He trained Anakin during the next outbreak of war, which threatened the Republic, and Anakin rushed off to become a Jedi while he stayed behind and assumed a mentor role, going to find Anakin only when it was clear that he was turning to the dark side, in an attempt to dissuade him from fighting. This is referenced in ROTJ:

"Come away with me."

"Obi-wan once thought as you do. You don't know the power of the Dark Side. I must obey my master."

The chancellor of course would have taken over Anakin's training at this point, and is sending him on dehumanizing missions and pushing him further than his physical body can take.

To the navigator idea, it would be good to reference this as Anakin's beginning. Obi-wan could have discovered Anakin when he was navigating a spice freighter, and it was there that he realized that Anakin was a great pilot.

Beru isn't really a presence in the OT, and I assume that the reason she isn't talked about was that Owen was the only one who knew Anakin before he left.