That was my stupid response, since yesterday I was exhausted, but the following one is my real one, and I hope it will satisfy you as far as my motivations are concerned.
The Chant of Light says "Magic exist to serve man, and never to rule over him". I will take this sentence as the basis of my reasoning, changing
magic with
kingship.
While I can see some political truth in many of Anora's lines, and she's undoubtedly a skilled ruler and a fine connoisseur of diplomacy and intrigue, I distrust politicians who are so eager to keep their seat, be it a throne or a Parliament chair. This mental attitude - this thirst of power, if you want - is in fact often coupled with a disregard of the social and civil issues that are so important to me and to this character of mine, Alqua. When I talked to Anora about the reasons why she should be on the throne, she only mentioned her foregoing familiarity with court's dynamics but never she mentioned her citizens and their welfare (not to mention her less fortunate citizens, like City Elves and it goes without saying that this whole issue is extremely important to my character, who still remembers what was it like to be raised in an Alienage). As such, I have little doubt that she would have been a marvelous queen, but did she really have what it takes to be a good ruler?
J. J. Rousseau wrote that "Each of us places his person and authority under the supreme direction of the general will, and the group receives each individual as an indivisible part of the whole" and called this simple rule the "Social Contract". Even without furthering his thoughts about Geneva and city-states, the concept of the free will of the Sovereign and the idea that the government must interpret this will and turn it into actual governement is pretty interesting. Alistair is a man rising from the common people of Ferelden, and a Grey Warden; he was raised by the Chantry, and yet he was given the opportunity to wander and see the world; as a child, he knew both the royal privileges and the social iniquities of the country. And he has royal blood, he's the last of the Theirin. All these qualities - heritage, knowledge of both aristocracy and common people, militar skills and inspirational prowesse, good understing of many different points of view (nobles, commoners, Chantry, Mages) - make up for a ruler Anora could never dream of be: she is not of the royal blood and her only area of expertise is Treasury and diplomacy -- necessary skills of course, but not the most necessary. Anora could have been Queen of Ferelden, but Alistair can easily be King of the people of Ferelden, and this, in my own personal opinion, is far more important that any other consideration.
PS: On a side note, I look forward, in another playthrough, to roleplay a character loyal to Anora, to the point of even letting Loghain live in spite of his crimes