I have read that talents will now be tied to each character life rather than souls and I believe that with the idea of traits passing on this is the better way to go.
My suggestion is to take the concept of genetic traits and turn it into boolean trees with pre-requisites for activation and combinations. Some talents may dominant or in logic terms: OR
Some talents may be recessive logic term: AND
A tree of these hidden traits will determine what abilities the character may secretly possess and by tying magical talents to other traits you can end up with a gene passed on but becoming inactive.
My example:
Mutation Slots:
The game would begin with a few hidden mutation "slots". They may be inactive but the character would posses a higher chance of their children developing mutations. Occasionally when a mutation would occur it instead adds or removes the number of slots with a slightly higher chance of adding more. The minimum number being One. These slots carry special Talents of Mann in the double pairing MUG/NULL as an example. (Magic Use Green and Null or Empty which would be the default) Additionally possessing mutation slots makes it possible to develop mutations via alchemy/spells or events. If a character does not possess enough mutation slots they will likely die if presented with a mutation. Having more slots also means a higher chance that the other talents mutate when they pass on becoming Null, a Similar Talent, or rarely becoming an entirely different Mutation.
Magic Use: This trait is stronger with each version that the character possesses. Having an active version of the gene grants access to the
magic use skill. Each time the gene is repeated after the first the character gains improved skill progression in Magic Use, can reach higher levels with the skill, has a higher chance to activate the talent and research new spells. Additionally this talent often improves other magical talents as well, improving chances of activation and potency as well as other factors. Having this talent does not mean the character has it active, and the character has to learn and research "spells" and rituals.
Magic Use Amber: Requires Amber Eyes or Eye Color Mutation
Magic Use Brown: Requires Brown Eyes or Eye Color Mutation
Magic Use Green: Requires Green eyes or Eye Color Mutation
Magic Use Blue: Requires Blue Eyes or Eye Color Mutation
Magic Use Purple: Requires Purple Eyes mutation
Magic Use Red: Requires Red Eyes mutation or Albinism
Magic Use Mutation: Requires Any Mutation and increases chances of Mutating. Using Magic has a chance of causing genetic mutations to themselves and sometimes even others (if they have this gene more than once) These mutations may have downsides, however on the positive side the gene itself may mutate into a more harmless version of itself or very rarely become inert...
Additionally Activation events are necessary, however it may be possible that powerful triggers cause a Dormant Magic Use Gene to activate changing the associated genes in the process... Mann's eyes have been known to sometimes change colors during the awakening but even other traits and mutations occur as well...
Other Magical Talents:
The other Magical Talents are also often tied to Eye colors although some of them may have other possible factors, additionally they can become active by having the Magic Use Gene even if "dormant". Having a Dormant Magic Use Gene can grant access to the magical talent while general Magic Use remains out of reach...
Healing: Requires either Green Eyes or Magic Use Green
Divination: Requires either Blue Eyes or Magic Use Blue Gene
Elemental Control: Either Eye Color or Magic Use trait associated with that element such as follows: Red is Fire, Brown is Stone, Green is Life (Plants/Animals), Amber is Electricity, Blue is Water, Purple is Shadows,
Teleportation: Requires Blue/Green/Purple or Red
Reanimation: The character can animate dead things
Medium: The character can interact with spirits etc.
Compel: The character can influence others minds magically
Enchanting: The character can create magical enchantments
Transmutation: The character can create changes in substances causing reactions, or causing entire changes
Shape-shifting: The character can transform into different creatures each form may have different trait perquisites while multiple copies of this talent or Magic Use may allow more forms by reducing a perquisite.
Wild Magic: Requires Magic Use Any chance of mutations upon activation, temporary random talents (Such as teleporting to a random location, raising undead, or starting fires) On the plus side
Magic Use talents can be activated without meeting other requisites... but the odds of random things happen is higher
Non-Magical Talents:
Non-magical talents could give other abilities and mutations such as gills with underwater breathing, fins with faster swim speed, greater physical height, bigger, stronger, weaker, slower skill progression, resistant or vulnerable to diseases/poisons et cetera.
Prodigy: All Skills advance faster before a set age cancels Dunce
Dunce: All skills advance slower until a set age cancels Prodigy
Longevity: Lifespan is increased by 10%
Mortality: Lifespan is shortened by 10%
Now to the other portion Lineage:
So with my example if a person possesses a Magic Use trait they may pass on the Magic Use ability. If the person they are using the child contract with has the same eye color or a magical ability they have a higher chance of the gene being active. Assuming all the other required gene pairings are homogenous having both trait pairs being Green for both parents for example, and both having only one set of the Magic Use Green gene it is only a 50% chance that the gene will pass on and be able to be activated normally (Exceptions may exist in rare circumstances such as being bathed in a magical wellspring)
Notably with this Magic Use can have potential side effects of Mutations: which may cause fear in citizens especially with mutations and wild magic. Additionally the powers may cause the character to create monsters or undead, or simply be a nuisance. This could cause some people to desire to destroy those who possess magic.
Powerful Talents require having more perquisite traits to activate or multiple mutations.
Basic Magic can become fairly common but still unpredictable as different genes require different traits. Additionally legendary magic would require having a stack of genes, activation and practice, often a lifetime or more. (Magic Use as a skill could still attach to souls as well, but simply be inert until activated)
Each Magical Talent may be attached to different attributes to determine the "Manna Pool" or whatever Aether or energy system is used to power Magic. If for example one grants points for strength, another for intellect, and another for charisma that would likely balance well.
Spells would require being researched by those rare few who possess enough ability.
I also hope that by presenting this here it doesn't create too much Meta and in any way discourage the creators from considering these concepts herein. Also tying these concepts to Lore or relevant traits would certainly improve things as well...