Jutsus that (still) aren't working:
Sage Mode Hashirama:
Wood Pillar.
Summoing: 5 Rashumon.
Wood Clones.
Advent of Trees.

Two-Eyed Kakashi:
Raikiri Cutter.

Naruto:
Kyuubi 1 Tail: Chakra Arm.
Adult: Kyuubi Chakra Mode (Requires Cache to be cleared).

Menma:
Unsummon Kyuubi.

Zetsu:
Wood Palm (Kaguya Lock).

Two-Eyed Obito:
Traverse Dimension: No Spawn points on Great Shinobi Battlefield, or Forest of Death (Kaguya

does though). Not ejecting Obito / Corpses upon death. - Works if a Kaguya exists in the game.
Traverse Dimension (on allies or enemies, comes up with Black Zetsu's text, not Obito's).

Princess Kaguya:
Dimension Strike.

Tobi Toggle:
Dismount Kyuubi. (Not sure on this).

Akatsuki Jins, Killer B:
Most jutsus, when switching to their bijuu forms.

Eternal Mangekyou Sasuke:
Fireball.

Rinnegan Sasuke:
Ultimate Susano'o: Ends auto after 10-15 seconds.

Adult Sasuke:
Does not count as a Rinnegan for Full Form Madara, or Kaguya.

Lady Chiyo:
Revive
Mother & Father Trap (Jutsu 0)
Cooldown issue; sometimes has 0 cooldowns at all due to her links.