They went with the story arc of Ash because they thought it would be a softer approach for kids. But look at Naruto, it's a show for kids but yet, as the story progresses, it gets darker and darker than the earlier episodes.
I really wish they made an anime out of Pokemon Adventures or The Electric Tale of Pikachu.
I mainly agree with Lil, an anime based around Pokemon Adventures would be too dark and edgy for kids. This is why they wanted to use Ash instead, cos he's more appealing to the kids that the anime is targeted towards.
I would like to have seen a Pokemon Adventures anime but sadly it won't happen due to those reasons.