Lilith Ex Bonisagus

Backstory: Lilith was her mother's long running research project, started before Lilith's birth. The purpose was to produce a magi who would live forever, yet still grow unhindered. Most importantly of all is that this magi would breed true. His or her Gift, and nature could be passed down to their child. This would evolve a better humanity. One that was ageless and Gifted. Lilith is that project, and so far the project has been completely successful. The only part that remains to be tested is heritability.

Lilith for her part had a banal upbringing. Okay she lived at a covenant, her whole life and was apprenticed, and was fed occasional pawns of vis, and underwent the last steps of the transformation process, but none of that was notably special to her. She took her vis just like the mundanes got their snake oil. She learned like any other magi. Her parens/mother put her through a strange rite, just like all those mystery cult initiations. Then she kept learning and studying before going off to join her own covenant to research at. Probably the most banal life story a magi could have.

What makes her... interesting is her superiority complex, and mission to have children. (That last part isn't as boring as it sounds.) She thinks that she is better than just about everyone else. She might pitty some people. (Her mother.) She might respect the work some people are doing (the Redcaps), she knows that some people are more powerful than her (archmagi), but she thinks that she is more than them. She is the first of the new more perfect humanity. Her sister Eve is her equal, having undergone the same process. (Although she is still technically going to remain an apprentice for 4 more years to their mother.)

Eve doesn't do a good job of keeping this quite. She really should, but she is derisive of mortals and most of the other Houses. The Quaesitores and Redcaps she respects. Both provide an essential service to allow research and works of the Order to continue. While it may not be providing the progress directly what they do is just as important.
On the Tremere while Lilith believes civilization and order are important, Tremere has the idea of it all twisted. They are totalitarian wannabes and that never truly works out. Their structure is based on individual force as the right to rule. Providing the military arm of the Order is nice, but everything else is so twisted.
The Mystery Cults have certainly found one way to progress, but it is a poor one. The mysteries are a dead end. The power cannot be spread to all. It is a shortcut to individual power, but not progress overall.
Tytalus is ridiculous. Conflict with others is not the source of power. Working towards growth is. Testing to see what is bad and what is good leads to progress. Brilliance, science, and effort. Writing books, building labs and research lead to power. Conflict may spur one forth and test ideas, but you need not fight others. That's just a good way to get killed, or have your books burned, or your lab destroyed. You want a seed to grow? You give it good soil and nutrients and water and sun. You don't give it harsh conditions. Humans are the same.
The Jerbiton are a tempting role to play. One always wishes to relax and bask in their works. And to be sure there is no point to progress if it is not enjoyed. The work of perfection is eternally undone, so we must stop on the path to drink it in. But to dedicate yourself to beauty and enjoyment? That just seems a bit selfish, even if truly it must be done.
Flambeau are awful. They don't form an organized military, and they actively seek out foes to fight. Yes militarization is essential for safety, but solo crusades do not a military make. And they provoke needless fights.

The second thing that make her unique is her quest. A lot of people have kids and a lot of people have apprentices. That's not unique. Lilith on the other had what seems to most an obsessive drive to gather books and perfect her lab. She wants her children to be the very best. They should have a book every day in the 15 years of apprenticeship if not being personally taught by her. Certainly a unique take on apprenticeships in the Order.

Note on the Theory of Evolution in Medieval Times: The whole theory flows quite reasonably from a few key observations about the natural world. Namely some traits help produce successful offspring, and these traits are sometimes heritable. Hence these traits will increase in proportion to the population. Sort of a breeding by nature or God as religious people would say. The ability to generate new species is not as obvious. It may not have been put together until Darwin, but there is no reason a Maga couldn't believe in "Natural Breeding" or Evolution. Nor would this need to go against God or the creation story. God's creations are self-improving. Just as a seed grows into a tree, a young species matures into a better one.

Character Sheet:
Bonisagus Mage, Age: 30 (19 apparent) Magic Might: 0 (corpus)
Characteristics: Int+1, Sta+0, Per+2, Pre+0, Com+5, St-2, Qu+0, Dx+0
Character Name: Lilith
Personality Traits: Proud+6,
Virtues: The Gift (Free), Transformed Human (Major) Puissant Magic Theory (Free), Hermetic Magi (Free), Good Teacher (Minor), Book Learner (minor), Great Communication2 (minor), Lesser Immunity: Effects that Lower Might Score (minor), Second Sight, Inventive Genius
Flaws: Incompatible Arts
4 (Intellego, all except Corupus/Vim) (minor4), Covenant Upbringing, Weak Spontaneous Magic, Close Family Ties, Proud (Major), Nocturnal, Low Self Esteem (Note: Ignore the Fluff on Low Self-Esteem. Instead think of it as her being too arrogant to put herself into it.)
Magical Qualities: Natural Appearance, Minor Virtue
Magical Inferiorities: Two Minor Flaws, Major Flaw, Suseptible to Deprivation

XP: 45 early childhood, 240 apprenticeship, 260 (2606xp from 9 years), 1 year of lab work
Arts: Creo 10 (55) Intellego 0 (0), Muto 4 (10), Perdo 4 (10) Rego 10 (55)
Animal 4, (10), Aquam 0 (0) Auram 4 (10), Corpus 4 (10) Herbam 10 (55) Ignem 4 (10) Imaginem 4 (10), Mentum 0 (0), Terram 4 (10) Vim 4 (10)
Total XP: 245
Abilities: Parma 3 (30) Magic Theory (Experimentation) 4+2 (50) Finesse 3 (30) Penetration 2 (15), Concentration 2 (15)
Code of Hermes 1 (5), Magic Lore 1 (5) Latin 5 (75) Artes Liberales 1 (5)
Philosophae 1 (5), Brawl 2 (15), Folk Ken 2 (15), Charm 2 (15), Awareness 2 (15), Atheletics 1 (5), English 5 (free)
Total: 300
Spells: 120 apprentice ship, 10 post apprenticeship
Aura of Ennobled Presence Level MuIm 10

Craft the Magi's Robe - Custom Spell
Rego Herbam Level 20
Range: Touch, Target: Individual, Duration: Mom
Crafts plant threads or fibers into an article of clothing. Requires a Finesse Roll to determine the quality of the garment.
Base 15+1 touch

Make the Tree Blosom - Custom Spell
Rego Herbam Level 25
Range: Touch, Duration: Mom, Target: Individual/Part
This spell makes a plant blossom, producing fruit and flowers. This does not need to be large enough to affect the whole plant.
Base 15 + 1 touch +1 Part

Walk Upon the Air - Custom Spell
Rego Corpus 15
Range: Self, Target: Individual, Duration: Sun
This spell lets the maga slowly move in any direction she chooses. At most she can move at a walking speed, although doing so requires her to actually walk.
Base 5 + 2 Sun

Lance of Flame - As Pillim of Fire, except the damage is +10 and level is 15
Creo Ignem 15

Touch of the Gardener - Custom Spell
Creo Herbam Level 30
Range: Touch, Target: Individual, Duration: Sun
Rapidly accelerates the growth of a plant, allowing it to reach maturity in but a day. The seed must still be planted in good soil.
Base 15 +1 touch+2 day.

Launch Brick - Custom Spell
Rego Terram 15
Range: Voice, Target: Individual/Part Duration: Mom
This spell hurls a stone into the sky in a high arc. If the maga has conviently shaped 1 cubic pace blocks of stone this can hit for as much as +15. Smaller rocks or stone do less damage, and dirt can even be used in a pinch.
The victim of the spell generally does NOT get magic resistance, the maga aiming with a finesse roll and gravity providing the momentum. The spell can target parts of objects so dirt from the ground or bricks from a wall are usable.
Base 3 +1 Stone +2 Voice +1 Part

Staff of Blessed Distortion-Lesser Item Level 13
Range: Touch, Target: Individual, Duration: Momentary
This staff grants a warping point to the object or person touched when the phrase "Blessing of the Four Realms be upon you" is spoken.
This staff may be used 6 times per day, and grants +1 to experimentation for laboratory work.
Base 5 +1 touch + 3 levels (6 uses/day)
Notes: The staff is made of metal twisted around a glove inside for a +3 shape bonus to affect at touch.

Two Tracti on Magic Theory Q14
Mathematical Analysis of Hermetic Forms v1.
Mathematical Analysis of Hermetic Forms v2.
One Tractus on Herbam Q14
The use of Herbs in the Lab v1.

Seasons of Laboratory Work
Season One: Write Tractus on Herbam
Season Two: Create the Staff of Blessed Distortion
Season Three: Write Tractus on Magic Theory
Season Four: Write Tractus on Magic Theory

This is cool and thought out in detail. One thing I'm having trouble with (and I'm sure this is just because I'm not as close to the character concept as you are, obviously) is trying to picture how she might change over time. This might be difficult to figure out given her "changed being" nature.

I often preach to young GMs to not design any plots whatsoever until the PCs have been created (at least in story oriented games). This sometimes needs to be said because often a GM will have a cool idea and want to design the game around it. That's cool, but the ideas should be directly related to the PCs, and the best way to do that is to see what the PCs are and react rather than force an unrelated idea into their stories. After all, if the story isn't about the protagonists, doesn't that possibly miss the point? I point out that characters are often created with built-in story ideas based on how the character is 'designed' to develop and what kinds of confrontations are likely to be had to spur that development (and dynamic character development is a key ingredient of story). When running, I often try to work with players to identify the 'built-in' stories of a character and how inner tensions or conflicts might be resolved (in various permutations - not marrying it to a single idea) so we can get a sense how dynamic character change might ensue.

So I'm wondering what she might learn and how she might change over time. What inner conflicts she has and what challenges might bring them to the fore.

So for example, this thing that she is is a result of something done to her. She assumes it is a blessing, but what might happen to change her mind on that? How might her understanding that she was manipulated as an experiment change her psyche? Is her overconfidence a psychological coping mechanism to deal with the abusive notion that she was an experiment? If this is true she's likely to be a very different person after having confronted this issue internally.

Just some (hopefully helpful) thoughts.

Hmm... she might learn to see the other Houses in a little better light. Room for conflict (of a sort) and growth by communicating with others. She has a skewed view of them to a large degree. She'll have more "external" stories though. The drive to get out and do stuff. Okay, talk with people and trade, but for her that's... an adventure, lets call it an adventure. All that is a lot funner in my mind than a psychodrama. Plus I mean really? "Whoa is me! I was given eternal life and godlike magical power by my mother. Whoa. Despair. Instead of letting random chance decide what my natural traits would be, she took a chance with her experiments. What kind of person would do that?!?" It would be really hard to change her mind on that. Because oh yeah, eternal life. Despite what T.V. tropes tells you immortality is not a curse.

Character sheet up. She is supposed to be able to do original research. So any ideas on what you guys want as the first target breakthrough?