I've figured out the whole Itachi thing.
Okay, I'm going to make a lot of assumptions here for the sake of my argument. First, some questions.
1) If Konoha ordered the Uchiha to be killed, why use an Uchiha to do it? Was it because only an Uchiha COULD do it, or because Itachi's strength was too great to throw out with the trash?
2) If Konoha ordered the massacre and Madara had a part in influencing Itachi, does Madara have connections with Konoha? (read: Danzou)
3) If Konoha ordered the massacre, why did Itachi leave as a nukenin? They could have easily covered it up. But Itachi admitted to it freely.
So let's take these assumptions, for the sake of the argument. Many answers are possible.
1) Konoha wanted to take advantage of Itachi's strength.
2) Madara had remaining connections in Konoha.
3) Konoha also wanted Itachi to leave as a nukenin.
Following this, we can surmise that it is possible that the massacre was planned with Madara, and then Konoha left Itachi in his care to join Akatsuki and work to their benefit.
But what would Konoha have to gain through Akatsuki? Like other nations, they want to use bijuu as weapons. We're assuming right now that Konoha is Danzou, the advisors, and the Third (He was senile). If Akatsuki could get those bijuu, they may have thought it was a worthy investment.
Another point: Yondaime hadn't been Hokage long when the Kyuubi attacked. So the Third had just come out of office. Coincidence? I'm sure Madara planned it very carefully, up to the very last detail. What if 'Konoha' knew about that, too? What if they'd planned to try to capture the Kyuubi once it had been lead into their territory? Yondaime wouldn't have known about that, though. Once Kyuubi was sealed into Naruto they had no chance of retrieving it for years afterward.
So when Akatsuki was formed and the possibility of getting the Kyuubi as a real weapon came along, the old folks couldn't help but jump on board. But what good would that weapon be to THEM if there were a lot of people who could control it? No doubt, if someone knew they could, they would jump at the chance and use the Kyuubi for who-knows-what.
So if they kill the Uchiha, there are only a few people who could even POSSIBLY control the Kyuubi, leaving them with no power struggles for him.
And that's my ridiculous theory.