Sounds fair, it is a lot, thanks. Any other things that stand out. I went to the middle ground for Natural AC
Medium Outsider (Native)
+2 Str, +2 Cha
Speed 30 ft
Darkvision 60 ft
Moral Exemption - Regardless actual moral alignment (Good, Neutral, Evil), the Nephilim is treated as both for the sake of which is more beneficial when meeting prerequisites for classes and feats. This allows an Evil Nephilim to take levels as a Paladin and simultaneously wield an unholy weapon (as per his actual alignment. This does not affect the Ethical axis of alignment (Lawful, Neutral, Chaotic), and that is handle normally.
The Nephilim still takes damage according to his actual alignment with regards to such effects. For instance, a magical circle vs Good would still affect an Evil Nephilim as if it were evil, and can ignore magic circle vs evil.
Developing Wings (as per Vestigial Wings) - Nephilim wings take a while to develop, at this rank, they do still grant a +4 on Fly checks.
Skill Training - Fly is always considered class skills
Languages - Common and either Abyssal, Infernal, or Celestial. Aquires an additional language equal to starting Intelligence Modifier from Abyssal, Aklo, Celestial, Draconic, Giant, Infernal, and Sylvan
Rank 1 (Divergent Path)
Celestial Resistances (Acid 5, Cold 5, Electricity 5), Gliding Wings (does not suffer falling damage and can glide 5 ft for every 1 ft fallen)
Fiendish Resistances (Cold 5, Electricity 5, Fire 5), Gliding Wings (does not suffer falling damage and can glide 5 ft for every 1 ft fallen)
+2 Charisma, Natural Armor 2, Moral Exemption now allows Nephilim to wield and use magic items as both a good and evil creature, whichever is more beneficial, and may even ignore moral limitations with items when using Use Magic Device.
Rank 3 (Divergent Path)
Wings (Fly Speed 40 ft (Average), Natural Armor 3
Wings (Fly Speed 40 ft (Average)), Racial Energy Resistances increase to 10
***Wings of Light and Shadow, Fly 60 ft (Good), Divine Power 1/day (Caster level equals character level for this effect). Amoral Subtype (the Nephilim can ignore damage and effects based on moral alignment, but still receives benefits from effects dependent upon it)
Increase one ability score of your choice by +2, Fly 80 ft (Perfect)
*For Wings of Light and Shadow, the physical wings that the Nephilim develops fade away, projecting into the different Transitive Planes (typically Astral, Ethereal, and Shadow), though still visible by a corona of pale light and flickering shadow. Because of this, the Nephilim can only be grounded through Dimensional Anchor. The wings cannot be affected otherwise, even with ghost touch weapons as they only link the Material and Ethereal planes. Despite their multiplanar nature, they are an Extraordinary ability rather than a Supernatural one. Visually, the wings can remain hidden unless the Nephilim is flying, but when on display, they shed an effect that acts as either a Light or Darkness effect, centered on the Nephilim.
Spoiler: Racial Feat
Crown of Light and Shadow
Prerequisites - Nephilim Rank 3, Wings of Light and Shadow
Benefits - When the Nephilim displays their wings, they may also manifest a Halo of similar energy as a free actions. This grants the Frightful Presence ability out to a range of 30 ft (DC is 10 + Half the Nephilim's level + the Nephilim's Charisma Modifier)