Okay...
Lets start with the simplest one. Every ninja above academy students should be able to walk on walls, and every ninja above basic genin should be able to walk on water. Everyone should be able to transform and make basic intangible clones. Everyone should have substitution jutsu added to their pages.
Itachi should get perception manipulation via Tsukuyomi (He can alter a persons sense of time along with all of their other senses including their sense of chakra and pain.) It should also be noted that tsukuyomi can destroy minds and induce mental fatigue. He can also display memories through genjutsu, but I don't know if that qualifies as memory manipulation.
Hanzo, Shikamaru, Naruto, and anyone else who has used explosive tags should get explosion manipulation for it.
Hashirama should get status effect inducement via darkness genjutsu.
Kabuto should get sleep manipulation.
Both Sasuke and Itachi should have paralysis and pain manipulation with sharingan genjutsu because of
this.
Orochimaru should have fear manipulation and paralysis via genjutsu.
Sasuke should have sleep manipulation via genjutsu, and stat amp for non CM2 versions of him pre-taka. Sasuke has also been shown to induce fear via genjutsu.
Neji can detect and partially deflect oncoming ranged attacks via releasing his chakra as seen here . He can also use gentle fist through chakra mediums as seen here
All sharingan users should get resistance to illusion creation and possibly mind manipulation (Since they have resistance to genjutsu and genjutsu can also be mind manipulation). They should also have Extrasensory perception via seeing chakra.
....I think that's it...anyone else have any others?