I *really* want the ninja to be a base class, but the main problem is the ninja having Sneak Attack ability. Everyone sees the Ninja as a rogue with monk levels or vice versa, but for me, the Ninja is actually a "Bard" without the knowledge, the singing and dancing because of Bardic Music. Let me explain: Bards make excellent assassins. If you remove all bard's abilities and add No Trace, Uncanny Dodge and Evasion and a weak version of sneak attack (instead throwing d6 dices, just add full Ninja levels to the extra damage whenever flat flooted or flanked).
Bard spells is very compatible with the ninja if you analyze it well, tough you have to remove the healing spells, and keep the enchantment and illusion schools because they are fine. That's my two cents :)