So, without further ado, allow me to rank each member and explain why they were all so damn cool.
SPOILER WARNING!
1. Pain
I honestly loved this character to death, from his past to his relationship with Jiraiya to the twisted relationship he had with Yahiko after his death to his status as a fallen chosen one to his parallels to Naruto.
Nagato is perhaps the only parallel in the series to not feel exceedingly on point. For example, you have Kakashi and Sasuke, Orochimaru and Sasuke, Jiraiya and Naruto - all of these feel like they are screaming at you that "hey, look, these are the past generation versions of these characters and a glimpse of who they might become." Nagato is a little more subtle. He shares a similarity with Naruto in that he was Jiraiya`s student and really wanted justice in the world, and had that "something special" about him that drew others to him, but his techniques, appearance, and personality are all his own.
He was hyped up for hundreds of chapters as the mysterious leader of the most dangerous criminal organization in the world, and those years he spent as a rainbow shadow only made his eventual reveal all the more hype. He lived up to it, too, killing Jiraiya of all people in his first fight, in what would go down as one of the coolest fights in the series.
Intimidating, capable, cool, unique abilities and a unique relationship with the main cast in a way that didn`t feel hamfisted. What a great character.
2. Itachi
Sasuke`s mysterious older brother. I can`t say anything that hasn`t been said a thousand times elsewhere already.
Part of Itachi`s appeal is that we are introduced to him gradually through the character of Sasuke. Sasuke is introduced as a genius ninja. We later learn he has an older brother who is thrice the ninja he is and more, but more than that, he`s incredibly dangerous and responsible for killing Sasuke`s entire extended family. Holy shit. Throughout Part 1 we always wondered - why would he do that? Is he just a psychopath, or is there some other reason? He had a mystery about him that made him appealing.
His techniques are also just really, really cool - turning into crows, black flames that burn even fire, skill in all three forms of ninja combat, the works. He really felt untouchable, even up to the end. The twist that he was good all along seems to be divisive, but I loved it. It made his already appealing character a hundred times better.
The loving older brother, the perfect ninja, the tragic hero, the solemn warrior. Itachi is just too cool.
3. Kisame
I`m a sucker for water based characters, so I liked him a bit more by default, but he really was awesome in his own right. His shark water bullets, his water prison techniques, his ability to summon tidal waves, his giant scary sword - this guy`s shark theme was done justice.
He has the added benefit of being one of the first members we see, and of being Itachi`s partner, so we as readers had that added attachment to the character. His past as a rogue ninja who lived in one of the worst villages in one of the worst times in its history is also interesting, especially since he shares a connection with his partner Itachi in that he was forced to kill his comrades against his wishes. He and Itachi are both the "ultimate ninjas" in that regard - sacrificing everything for the mission. The scenes the two of them share have a unique feel when compared to the other Akatsuki members, where there`s a sense of mutual understanding and respect between them, but also a distance that precludes any sense of real friendship, showing that they`ve chosen to remain emotionally isolated because of their pasts.
Kisame held his philosophy until the end. Was he a good person? Not really, but he was empathetic and admirable, to a degree, despite his generally bad actions. Awesome voice actor, too.
4. Sasori
His resurrection arc excluded, Sasori is an amazingly terrifying villain. He first appears monstrous in the body of his puppet, and then after learning his past, we discover that he is an actual monster who turned his parents and even the Kazekage into puppets.
He was an appropriately psychopathic villain for a criminal organization, and he also gave us more insight into the Sand village and its history. I loved his dynamic with Deidara as two artists with conflicting ideas about what art is. His battle with Chiyo and Sakura is honestly one of the best fights in the series, especially when animated.
I don`t have much to say other than that, as he had the shortest run of any Akatsuki villain, but he definitely served his role well while he was there. What a great introduction to the rest of the organization in Part 2.
5. Deidara
Technically our first glimpse at the rest of the organization after their tease in Part 1, Deidara enters the scene by... fighting the new Kazekage, which is now Gaara, and defeating him. Whoa. That`s how you make an impression.
His exploding clay and brash, youthful arrogance give him a generally loud aesthetic that the other solemn members lack, and all of his techniques ended up being really creative for running with such a simple theme, which basically amounts to "statues that explode." His relationship with Sasori was great, but I also loved his relationship with goofball Tobi, which was often hilarious. Had a great fight against both Gaara and Sasuke. Loved how he`s one of the first Stone Village ninja we see.
6. Konan
An origami ninja? Awesome. Her past with Pain and her status as second in command and her angel motif gave her a lot of presence. Unfortunately, she didn`t get any really great fights. I put her higher because as a character, conceptually, I thought she was really cool, regardless of how she ended up being used. Great design and overall aesthetic. She looked very "heavy metal," and stands out quite a bit compared to the other female characters in the series.
7. Kakuzu
A ninja from an older time who keeps himself alive by stealing hearts. A man who cares for nothing but money. A cold and calculating ninja who doesn`t have the time for pleasantries or relationships. Kakuzu is the kind of villain I`d expect to see in a series about good ninjas vs. bad ninjas. He reminds me a bit of Zabuza in this regard, where he just feels like he fits the premise of the series.
Unfortunately, I didn`t find either his design, role, or abilities to be all that interesting. I don`t actively dislike this character, but I don`t find much to praise about him, either. Maybe it`s because he got shoehorned into a fight with Naruto and Kakashi in an arc that wasn`t about them.
8. Hidan
I found this character actively annoying. Sure, his death god theme was kind of cool, and fitting for the general atmosphere of Akatsuki, but his personality was shallow and his past was nonexistent despite being immortal. A cultist who serves an evil god who was able to become immortal by serving said god. The religious aspect felt out of place in a series about ninjas, especially because this "Jashin" is never explored any further and ends up feeling more like a plot device to make this particular character unable to die.
His whole schtick is that he`s unapologetically evil, but it fell a bit flat because it`s only ever explored at face value. The best thing about this character is that he let Shikamaru have his time in the sun by defeating him.
9. Zetsu
He was sort of creepy and appealing as a weird flytrap man who gathered information for the organization, but nothing good came out of this character, ever. In fact, everything involving him could probably be considered a low point of the series. The whole thing with White Zetsus being clones and Black Zetsu being "the will of Kaguya" and Zetsu fusing with a teenage Obito and... yeah. I really didn`t like him.
With only two real duds out of nine characters, I think Akatsuki was the bee's knees, my friends.
