Board Thread:Naruto Discussions/@comment-3965545-20160202201023/@comment-3965545-20160203074425

There is literally no reason at all other than the disease that his chakra levels would be lower than Kakashi's who's transplanted Sharingan is the reason for low chakra in his case. Itachi was apparently taking medicine for years so if that was more specific we would know exactly how many years.