Abilities and passives you can gain through the course of the game?
First off, the Master traits:
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.
Second, the hidden Velvet Room quest awards the Touch of Adonis; its effects are mentioned in the wiki entry for the room:
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Third, there's two traits you can gain from completely reading books that can be found in Aria Bianchii's New World Order quest, when you
loot them from the Palace in the Rebellion path. The books are Sundering Minds (trait gained:
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) and The Mare (trait gained:
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). No idea how the master of mares actually activates. I assume it's a passive effect.
Lastly, there are the Implants from the
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in Crystal Heights and from the
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in the Mastersphere space station. They're pretty self-explanatory.