Eh no offense but that's a pretty weak example, I think a more appropriate one is Udina ends up in the Human Councilman position anyway even if you awarded it to Anderson. Perfect example of retcon.
I dunno, considering that ME2 showed that Anderson really hated the job and his Shadow Broker dossier implied he'd begun to develop a slight drinking problem due to the stress... it's not that surprising that he decided to quit and go back to the Alliance.
Furthermore being an Admiral in the Alliance means that Anderson can actively help Shepard, something he couldn't do as the Human Councillor, as the other Councillors would have likely forced him to step back to avoid a conflict of interest.
We're given hints that Hackett and Anderson pulling strings and calling in favours are main reason that Shepard has spent the intervening seven months under house-arrest and relieved of duty while pending trial, rather than having been thrown under the bus in a kangeroo court to appease the Batarians for the destruction of the Bahak System.
It's still a retcon, I agree, but it does thematically make sense why Anderson stepped down when he did.