Is this really intended as a jack-of-all-trades, or as a wildcard's wildcard? Where do you see this character locking into a three to five character party?
The Incarnate's role is that of someone who isn't sure what they want to play, but knows that they don't want to multiclass very much. Compared to a Sage, the Incarnate cannot:
-Gain 4 more skills than normal, only gain 'floating' skills like the Priest
-Reduce the time it takes someone to utilize a skill
-Replace a skill bonus with a better one from an ally, or replace an ally's bonus with their own
-Gain temporary Chance feats, arguably one of the best feat groups to get temporary feats in
-Recover the vitality of allies
-Increase the Starting Action Dice of the party
-Benefit from the GM granting a 4-AD-worth boon to the whole party
Instead, the Incarnate can do the following:
-Improve their attributes slightly and gain semi-mystical ability with their Body/Mind/Spirit
-Gain 5 bonus feats over their career (6 if they have the Core Ability)
-Gain Renown 4 times (useful if you're keeping Prizes or trying to schmooze through Favors, not too important otherwise)
-Round themselves out with useful self-boosters
-Gain extra wounds
-Gain a second specialty
Really, the only thing they share with the Sage is the Cross-Training
ability. If there is an ability I would trade out, it would be the Life of Discipline
ability with something a bit more focused and less choosy. Maybe they could get a bonus feat chain + improved skill caps for a skill like the Lancer, but I don't know what feat chain or skill to grant them.
I see this character as several things...
-A Drake that wants to improve their flying and fire-breathing capabilities so that they don't need to rely on unarmed combat or magic to be a fighter
-An Elf who wants to be semi-decent at magical abilities, archery, tracking, and rubbing elbows at parties without needing to have two or three different Base Classes
-The human who is half-angel and half-devil, whose inner struggle is the stuff that legends (and Subplots) are made of
-The Unborn that improves himself as he adventures; he gains flight after a little bit, then he gains some in-built tools to use, and then he makes himself some extra hands to be even better at building or fighting
-Other homebrew races that don't have much, or any, other support beyond their original creator
Overall, these are character concepts that are difficult to accomplish without multiclassing heavily, and I wanted a class that could cater to those sorts of characters. It fills a niche that does not yet officially have an answer, and I don't see anything wrong with the class balance-wise (I could be wrong of course, since balance isn't my best skill).
That is where I see the Incarnate in a party, as the character whose player wants a little bit of everything without being Magical (either Arcane or Divine) or a Chance-and-Action-Die monkey (the Sage).