Ok, call me crazy or sleep deprived (cause it's one in the morning) but I feel like Days put some sort of strange emphasis on Zexion's elimination. On day 72 -a day after Axel returns from C.O- Axel informs Saix that he disposed of Zexion, but not Vexen. The only other mention of this we see is on day 117, when Saix tells Axel he has to return to C.O. Only THEN does Axel bring up Vexen. Maybe Axel mentioned offing Vexen before this, but we only see this mention quite a number of days after Axel tells Saix about eliminating Zexion. I don't know why, but that statement "I disposed of Zexion" and ONLY mentioning Zexion makes it seem like Zexion was the major obstacle for them and their plans. I get that Zexy would have probably found out their plans and ratted them out to Xemnas, but Vexen could have as well. But Vexen didn't seem to be as much as an obstacle for Axel and Saix as Zexion. Why? Why was Zexion so important to Axel and Saix? I just get the feeling there was something more to it. PLUS! In the 1.5 cutscene, when Axel tells Saix about Zexion, the music stops. Which is usually a sign of importance. So there's that. WHY IS HE SO IMPORTANT? It's been bugging me!

Because Zexion was poised to become the eventual (public) second-in-command (from one of the JP-only character reports); Axel and Saix decided to nip that problem in the bud, as it were.

 

 

As he shares something like a master-servant or teacher-student relationship with Xemnas, like Saix, he is a character with strong connections. While he was the superior in that regard, perhaps that was ultimately his downfall. It is likely that if Marluxia and Axel had not betrayed him in Castle Oblivion, he would have played a central role within the Organisation.

Why ISN'T he so important? He's the (in my opinion, which may or may not be biased because he is my favorite Organization XIII member) smartest of the bunch. I believe he is not necessarily more intelligent than Vexen but definitely smarter. A better tactician in that he thinks things through. Not only that but he was also taught by both Vexen and Ansem the Wise directly as seen in BBS. He noticed in 3D some new piece of possible important info, that we still don't know thanks to Leas interruption. And with those smarts he probably would have noticed Axel and Saix's plans to climb the ranks of the OrganizationHe was able to command Lexeaus for cryin' out loud. And if it weren't for Riku's apt for darkness he would've beaten just about anyone, I think.Or maybe they just wanted to climb the ranks since he's 6 and Axel and Saix are 7 and 8. Maybe because he's not "strong" but he was the most difficult adversary for them given his abilityIenzo/Zexion is important because he is a badass!!!

Because Zexion was poised to become the eventual (public) second-in-command (from one of the JP-only character reports); Axel and Saix decided to nip that problem in the bud, as it were.

And the this...

It's probably because of how young he is and obediant he it that Xemnas chose him due to how easy it is to take advantage of him.

Because Zexion was poised to become the eventual (public) second-in-command (from one of the JP-only character reports); Axel and Saix decided to nip that problem in the bud, as it were.

So we almost got Zexionnort? Damn it I wanted to see him like that!

Because Zexion was poised to become the eventual (public) second-in-command (from one of the JP-only character reports); Axel and Saix decided to nip that problem in the bud, as it were.

 This please^^ 

 

Also you already listed the other reason..As Axel said himself, Zexion found out too much. He was a problem.

Why ISN'T he so important? He's the (in my opinion, which may or may not be biased because he is my favorite Organization XIII member) smartest of the bunch. I believe he is not necessarily more intelligent than Vexen but definitely smarter. A better tactician in that he thinks things through. Not only that but he was also taught by both Vexen and Ansem the Wise directly as seen in BBS. He noticed in 3D some new piece of possible important info, that we still don't know thanks to Leas interruption. And with those smarts he probably would have noticed Axel and Saix's plans to climb the ranks of the OrganizationHe was able to command Lexeaus for cryin' out loud. And if it weren't for Riku's apt for darkness he would've beaten just about anyone, I think.Or maybe they just wanted to climb the ranks since he's 6 and Axel and Saix are 7 and 8. Maybe because he's not "strong" but he was the most difficult adversary for them given his abilityIenzo/Zexion is important because he is a badass!!!

And the this...

 Really I wouldn't call him the smartest - Axel himself outsmarted him in CO. Also Lexeaus listened to him outta respect and friendship bc of their ties as somebodies

Also you already listed the other reason..As Axel said himself, Zexion found out too much. He was a problem.

But what was it that Zexion found out way too much of? Cause that always bugged me.

But what was it that Zexion found out way too much of? Cause that always bugged me.

 

Axel and Saix's plans and rebellion. He noticed something going on and suspected them. The events of CO would've looked bad for them if it got back. Little did they all know however is that Xemnas already knew about Saix and Axel and just didn't care. Stated by Nomura himself.

Axel and Saix's plans and rebellion. He noticed something going on and suspected them. The events of CO would've looked bad for them if it got back. Little did they all know however is that Xemnas already knew about Saix and Axel and just didn't care. Stated by Nomura himself.

 

Because Zexion was poised to become the eventual (public) second-in-command (from one of the JP-only character reports); Axel and Saix decided to nip that problem in the bud, as it were.

Well hot damn! Thanks!

I thought it was because he is sexy (fan's words - not mine)

Zexion always struck me as easy to command or take control of: In the manga of CoM, he was almsot acting like a nursemaid/mother to the others, which was pretty off. His illusions were probably getting too powerful, and along with the threat he might know to much, maybe he messed with something earlier, or tried to confront Sora too early. The fact he was young, and fairly naive acting, aided the idea he might've been up in line for the new second, so that meant bye bye, Zexy. 

 

Because Zexion was poised to become the eventual (public) second-in-command (from one of the JP-only character reports); Axel and Saix decided to nip that problem in the bud, as it were.

Oh.. 

It seems like Zexion was like a living lexicon, gathering information. He knew stuff. This is also shown in the cutscene in KH2FM when Xigbar asks him about Xemnas and what he is doing in the Chamber of Repose.