I post slot about itachi having his illness due to rinnegan trying to manifest within him. As an emerging power of something known to have steep physical cost his body and health suffered. I posted this idea in the illness thread and scoff at this idea all you want but my next point will challenge and perhaps win you over to this idea.
Anyway, we don't know everything but through direct revelation in the manga we believe rinnegan to be evolved from the sharingan or more correctly, the sharingan diluted piece of rinnegan that can be reestablished through the right conditions, conditions often riding on destiny itself. At this time we have the impression that an uchiha who masters the power of sharingan, masters mangekyo, and possibly also eternal mangekyo,.then that uchiha is candidate for awakening rinnegan. We believe madara to be the best precedent for this theory and ksbuto's hypothesis backs this up.
Itachi, then, had all known requirements except the eternal mangekyo. Perhaps simply possessing shisui's eye caused the early stages of manifestation or better yet, which i believe. The, excuse me for my lack of. A better term, "biological groundwork" for rinnegan begins along the mangekyo stage but completes at the ems stage. The rinnegan is a power and curse of sorts and symbolically and thematically would call the strongest sharingans back to it so to speak and at a certain point, outright demand the ems.
Itachi had this rinnegan groundwork and knew it and what it meant. He had to keep it a secret unless he become a target, call too much attention to himself or upset the balance of power in akatsuki or elsewhere, keep in mind that many ninjas or lords thought rinnegan only a myth! Knowledge of itachi, the branded criminal, would disrupt the norms to a degree that doesn't require discussion. It also makes sasuke a target and itachi needs to complete his manipulations with him to push and also protect him.
Now, IM running out of time here but ill rush my conclusion and let you think for yourself.
Itachi knew he was manifesting rinnegan, he had to keep it a secret and he knew it was making his body ill (they called it a mystery illness,that zetsu) He knew ems is required to complete it. He pushed sasuke to the mangekyo level, he knew what was in store for sasuke but let sasuke remain ignorant. Sasuke can not handle certain truths all at once, much less risk the lust for rinnegan power even now where we are i. The manga.
He keeps his rinnegan groundwork secret from tobi, who itachi knows isn't madara, and who doesn't know the truth of rinnegan even if given to him, gjosr aren't his natural eyes after all. He keeps it a secret to ensure tobi gives his eyes to sasuke. I repeat, this is important, he kept his rinnegan secret to guarantee that sasuke recieved his eyes! Itachi has big hopes for sasuke and understands his epic role in the shinobi world he will play, he knows giving sasuke ems with his rinnegan groundwork eyes will complete the.recipe so to speak and sasuke will inherit the rinnegan.
Well that's my answer to the mystery illness and how i have plugged many holes for myself regarding itachis behavior but i think its a solid theory in line with the characters involved and stays true to how the story is progressing. IM itching to argue with you now since ppl thought this idea was stupid when proposed last summer. The best part of itachi is that he understands the destiny of sasuke's role, just not the path to it. With that knowledge he carefully manipulated sasuke into being among all the Gillian's itachi knew were villians to destiny. He snuck sasuke to their doorstep with a secret rinnegan package nobody knows about. Itachi has effectively help set the stage for the final confrontations. I was never a fanboy but i really enjoy the handling of the character and this, moreso than anything else, completes the last point he made during his time back as an edo, that you have to forgive yourself and let others do what you cannot. It makes sure sasuke ascends as an avenger by doing what
itachi couldn't. Wield the ultimate power against those TRULY responsible for messing with his clan, his village, and his world.
Edit: just got back from midnight premier of Batman. What i want to add is that i am a writer. My brother is a published writer, i find i enjoy how kishimoto uses classic ideas and themes next to real world religious stories and cultural lore. Naruto is rarely just relying on arbitrary developments or blind whims. Case in point, kishi has made the uchiha a timeless and universal idea and theme. Uchiha, if you may excuse my necessary redundancy, are "literal figures " of "blind with power" and characters like naruto are "illuminating fire". These are two common themes used for ages in the art of story telling. Kishi does not deviate from themes once he assigns them! Proof is in the pudding, folks, uchiha who advance in power will go blind. The most important symbol kishi ever did with this was the panel of shisui during the recent itachi memory flashback. Shisui was PHYSICALLY blinded but he could see better than any other uchiha figuratively! He sacrificed his power and physical sight because he saw what was revealed by "illuminating fire", meaning Jonah's and his will if fire. So, if you think that shisui is tobi, you're dead wrong because he was used as powerful symbol to illustrate the idea. kishi will not stray from a theme without a good reason or complementary idea.
Itachi was not blind but his flaw was not understanding himself correctly or bring closure to his ordeal until after the "illuminating fire" crossed his path (naruto) itachi could finally understand what he needed to realize about himself and depart from his brother after dealing with his mistakes. His lecture to kabuto is kishi cementing this. Its also obvious by the well known declaration given by naruto of using his wind to fan sasuke's flame (the flame will shine brighter, its more theme play) as for rinnegan developing in itachi.. when kishi reveals shinobi history he sometimes have a scenario from the past play out in the present (history repeating itself). These parallels are constructed, however, with key differences to make a greater point. Madara took his brothers eyes for power, he was truly blind and his behavior against the Kate's proves it. Parallel, itachi sacrifices his power/eyes from the point of view if one illuminated. And he knows naruto will be his light leading sasuke from the darkness. This is why itachi has indirectly and also in cases, directly, steered sasuke on a path of power leading and relationships with evil villians. It puts him close to the reasons why the world is at risk of plunging into their darkness. Itachi will let sasuke do what he could not. Finish the rinnegan he started and defeat the evil with his power under naruto's light which itachi knows will be visible to sasuke in due time. It goes on and on but is important to keep in mind when developing any sort of speculation or opinion concerning anything uchiha.