Alright after much time has passed I finally decided to re-write this theory, and to fortify it better.
Now my theory that Im proposing is that Madara is controlling Itachi from the shadows. Now Im not exactly sure in which form he is doing this, however Ive thought of a few.
The main one Im proposing is that Madara is controlling Itachi from the inside. In which Itachi and Madara are sort of sharing the same body. I believe that Madara has not only been training Itachi for most of his life but teaching him also. Itachi is by far one of the greatest genius from Konoha and has demostrated that countless times by surpassing all his age at the time. Now I understand its not impossible for him to simply be a genious considering that Kakashi became a chuunin at an earlier age, and its hinted that Gaara surpased him when taking the forest of death test.
Now back to my proposal
To begin with is the ever popular phrase
"I killed them to test my container"
Now this phrase of "container" is as uncommon as it comes... maybe not
actually Orochimaru uses this phrase all the time when hes refering to his new body
Itachi also mentioned that he continued to act like the older brother Sasuke desired.
I believe that around that point he was nearly fully possessed by Madara, other examples where he was fully possesed are...
and when he regained consciousness, or at the very least returned the act for Sasuke
Also Judging by the way he acted during chapters 220 and 221, you can notice the major change in his personality occured around the time he joined ANBU, now ANBU is far too secretive and the manga has shown next to nothing so Ill just leave it that when he was strong enough to join ANBU it seemed he began to distance himself.
Itachi also mentioned how he despised all the rules set by the clan, all the limits that were holding them back. Itachi being only 13 at the time couldnt have possibly its potential.
Itachis Mangekyou Sharingan, While he did hint that Shisui helped him get it, he never directly mentioned he killed Shisui, but he did deny it. Also considering the other brash actions he did, admitting to killing Shisui would seem almost like a drop in the bucket.
By the time Itachi was interrogated by the 3 Uchiha police, he already had the Mangekyou, not to mention that if we do believe Shisui commited suicide, there would have to be a reason. I believe that Shisui commited suicide after Itachi used Tsukuyomi on him. Thus making the letter that was shown to be actually written by Shisui even if it could have been forged.
Note - I may have forgotten a few things in the re-write