If the Ninja subclass was a Wizard subclass, you could then have something like the Shinobi in the Naruto anime. At 2nd level, you could give them some additional proficiencies in Light armor and weapons typically associated with the Monk. You could also have it where they gain bonus spells at 2nd level based off of their Nature Affinity (Air, Earth, Fire, Lightning and Water). As they go up in level, they could expand their Nature Affinity by picking up another element or two.
As for the rest of the subclass, it could be designed like the Bladesinger Wizard, but instead of having the Wizard lean Fighter, it instead leans towards the Rogue class.