Just tossing random ideas off the top of my head here. I am by no means an expert on FC mechanics, so I'm not sure how these will go over.
Would it be possible to make it a Point Buy system? Mages get Spell Points for spells. What if Incarnates/Totemists got Shape Points? These points would in effect act just like XP for the purpose of "buying" Natural or Extraordinary attacks.
Then you could use a Spellcasting-like skill (Incarnation?) to make a DC, just like casting a spell for success/failure in attaining the required ability.
"Incarnations" (i.e. powers) would be learned like spells: X number to start and +1 for each new rank in the control skill. You can't take on a quality you haven't 'researched' and know.
Incarnation Adept: You learn 2 additional 1-XP NPC Qualities as Traits. Also, once per scene as a free action, you may spend and roll up to 3 action dice to gain a number of incarnation points equal to the result. These action dice cannot explode.
Form of the Beast: At Level 1, you may purchase ranks in the Incarnation skill, learn NPC Qualities as Traits, and take on Traits you know.
When an incarnate gains his first Incarnation Points he immediately learns a number of NPC Qualities, known as Traits, of any XP Value equal to his Incarnation ranks. Depending on the nature of the setting, these traits may be chosen or randomly assigned by the GM. Once learned, traits may not be exchanged. Note that knowing a trait doesn’t mean a character can assume it — the limits of incarnation assumptions are set by a character’s class.
Losing and Regaining Known Traits: Should an incarnate’s known traits decrease — temporarily or permanently — he chooses which traits are lost. Should this number later increase again the character must relearn the lost traits before he can gain new ones. Lost traits may be relearned in any order.
Incarnation Points: An incarnate assumes traits by spending incarnation points, which he gains from a number of sources (primarily class). He pays incartnation points equal to a traits NPC Quality XP value each time he tries to assume it (and doesn’t regain them even if his Incarnation check fails). Incarnation points are fully recovered at the start of each scene.
Not sure how many points they should get as they level. This is something we'd have to play with and see what is balanced. Maybe half a mage's SP?
Incarnates and other incarnation users can spend skill points to purchase ranks in the Incarnation skill, which is only available to characters with a set requirement?. Incarnation operates like any other skill.
Tools: An incarnate without an incarnation totem is considered untrained even when he has Incarnation ranks (see New Equipment).
Knowledge: Monster traits; shapeshifitng techniques
Acts exactly like Spellcasting, but with the DC based on the XP Value of the trait, rather than on spell level, and down one slot so a 1XP Trait = 0 Level spell.
Incarnate Level 1 Example: Let say our level 1 Incarnate puts 4 ranks into the Incarnation skill.
He knows 6 Traits NPC Qualities, 2 of which have to 1XP NPC Qualities. Lets say he chooses the following traits: Darkvision I (1 XP), Fast Healing (1 XP), Fearless I (2 XP), Claw II (4 XP), Natural Defense [lethal] (5 XP), and Invisibility (8 XP). At first level lets say he has 1 Incarnation Point and chooses to spend it to take on the Fast Healing trait for the scene, needing a DC 13 to take on the quality.