I guess I got lucky all around with Kingmaker. Having read through the entire AP beforehand, I created numerous side-stories and really let the players center a lot on their own characters' stories, as well. I introduced the BBEG way earlier and had an involved story line that centered the AP around fey from Book Two. One of the major problems I have with APs generally is that your characters have no time to develop beyond the story the AP is telling, because everything just feels like it must happen so quickly. Kingmaker had no time constraints on it at all, which enabled the players free reign on all sorts of development time! I've run half-a-dozen PF APs, and I thought this one the most freeing from both a GM and player standpoint.
As to the kingdom building, I was lucky on that too. Most of my players weren't interested in it at all, save one, who basically was put in charge of all of it. He then poured over the math of it (which he loves) and made the vast majority of the decisions. However, he wasn't the king, so the group role-played through the decision-making process, with the one player describing to king and council what was happening in the city, then getting any input the others wished to give on where they wanted the kingdom to go (with special emphasis placed on the king's decisions on it). These council sessions lasted between 10-15 minutes apiece. We also did kingdom rolls and all of that during these, with different players rolling for the different kingdom stats, and events would get put into the roleplaying for the month so as to better work in with the players' individual stories. Thus, our kingdom building was incorporated into the role-playing of the game, which worked beautifully and kept the whole party invested with a part of the campaign that they cared little for because of the numbers game.
I will say that Kingmaker requires a ton of time for the GM, but if you're able to put in that time, you won't find a better AP in the line for 1E. That's just my take, however. I do agree with some of the others here on other APs. Reign of Winter has a great story, as does Curse of the Crimson Throne, which I'm currently playing in right now.