We keep going to this Akatsuki is "evil" standard, but we have yet to see any real solid evidence of such. Don't get me wrong they are antagonists, but that doesn't mean they're evil just something in Naruto's way. I really can't help to think that it is possible that Akatsuki may have some kind of a higher purpose to captureing the bijuu. I mean we know Orochimaru is evil, and I feel Danzou the leader of the root division is intent on regaining his former power in Konoha if not more power. Anyway back to the topic, I'm just bothered by a few things that we have seen so far in their story involvement. While we know that we have seen alot of "attempts" to harm ninjas that are in their way, I have noticed a lack of commiting any actual killings directly. The thing that bothers me the most is that the Akastuki had already taken Shukaku from Garra and yet they intended to take Gara with them after the Konoha ninjas had infiltrated their hideout. I see no value to Gara's corpse, perhaps they have some revival ninjutsu's of their own. Yes I'm aware that all of the ninjas within their ranks are criminal ninjas, the Akastuki members themselves are all S class according to Jiraiyai.
We know of what we believe Itachi has done, but we must remember that Sasuke had arrived toward the end of his "actions" and while he did take credit for the genocide of the Uchiha clan, he even showed Sasuke what "happened" with the Mangekyou. Though he could have easily been lying especially if by chance Itachi felt that he may lose to the "real" perpetraitor, he would definately not want his little brother to pursue and be killed by the real enemy. I mean you must consider the fact that those with bloodline limits have been killed in the country of the hidden Mist(other countries too I'd bet) due to the threat they posed so it is possible that if someone had seen Itachi's MS it could be seen as a potential threat, though this is just some speculation.
Now on to Sasori, Chiyoba was intent on saveing him. I'm sure her wisdom would tell her that that would be a waste if he where indeed some evil villian, true he turned his parents into his first puppets, but that seemed to be common knowledge. So then why would Chiyoba have not dealt with him when he was younger rather than wait, simply put we don't know what had happened to Sasori's parents before they where turned into puppets his actions could have had the intent to save his parents or even bringing them back from the dead. I mean go back to Naruto chapter 268 pay attention to the structure of page 15, in the second panel we se him looking at two picture frames and then structures down to him hugged by his "parents" which to me shows that they had died before he had turned them into puppets. This would also explain why one so proud of all of his creations would "abandon" these two puppets, because they held a sentimental value he could not use them in combat for fear of damaging them. I mean he had not caused them serious damage during the fight even though he knew all their tricks(this being said I think he could have easily dismantled them if he chose to do so).
Also this would leave the door open for the possibility that Yondaime is the Akatsuki leader, if he is still alive. Especially if he had been keeping an eye on Naruto and decided that being a container for the bijuu was too much of burden for anyone to bare. After all we know that their leader did not want Kakashi to be killed, which is some indication that this is possilble since I'm sure Yondaime would not wish any harm to come to one of his pupils. That being said this would also increase the chance Tobi is Obito. Though it is hard to delve too far with out more information on the rest of their members.