I ultimately decided clans should be based around possession of a particular Disicpline, not unlike Requiem. However, unlike Requiem, each Discipline (except the physicals, which are considered universal) gets a Clan, and only one Disicpline defines a clan. Generally, I wanted to go with the basic seven, but they need to be paired with my modified disciplines, which requires a couple of changes. Fortunately, I also found the Tzimisce and Lasombra as compelling stand-alone concepts, perhaps more so than the Brujah and Gangrel. So I switched those out, oh, and I also decided to generally use what I consider a niftier name-set. This also associates a weakness with each Discipline, and I decided that there would be a greater and lesser version of these. The greater version affects the clan that inherits it, and the lesser affects those who learn it. This might come down to more of a primary and secondary effect, which would cause the native clans to have both, and those who otherwise learn the discipline would only get the secondary.
The Clans:
These aren't necessarily "final" just current ideas.
Arikel - Majesty
Primary weakness: Fascination - basically as the Toreador disadvantage, specifically Requiem version.
If rolling Resolve, must gain successes equal to Majesty level.
Secondary: Obsession - as the Assamite Vizier weakness (Possibly reverse these).
Nosferatu - Bêtiare
Primary: Monstrosity - inverse of striking presence, -2 on appearance related social rolls, also the Nosferatu disadvantage from Requiem.
Secondary: Beastliness Bêtiare level adds to Beast/Blood Potency rating for purposes of comparing it to Humanity. The character also acts as if his Humanity is 10 minus Bêtiare (or his actual Humanity if it is lower) for purposes of gauging pools for interacting with mortals.
Malakh - Auspex
Primary: Seen too much - Malakh have an inherent mental instability caused by their supernatural insight, and all begin with one incurable derangement. Any result aside from Success is likely to set off the derangement some time that night. Operates as the Malkovian weakness from Requiem, substituting Auspex for Dominate.
Secondary: Forbidden knowledge. Those with auspex are more likely to acquire derangements when suffering humanity loss. This operates as the Ventrue weakness from Requiem.
Veddartha - Dominate
Primary: Inhumane - On a degeneration check, they are -2 to the roll, just like the Julii.
Secondary: Humanity and Empathy cost extra XP equal to dominate at each level.
Khaibit - Tenebrus
Primary: ?? - possibly the reflection thing, unless that is used as a general vampire property
Secondary: Fleeting Shadows: Other vampires are impeded by daytime and sunlight. Khaibit, having brought forth their shadowy nature, are harmed by it. The penalty normally taken by other vampires (which is actually the amount of damage they would take per round in either Requiem or Masquerade) is taken as bashing damage when exposed to sunlight. Additionally, they experience Rotschreck from Sunlight as well as fire (other vampires in my version of the game do not Rotschreck at sunlight)
Tzimisce - Protean - bestial features
Primary: Possibly the standard Tzimisce disadvantage.
Secondary: Bestial Features.
Each frenzy evokes a beastial feature or behaviour from their regular repertoire for a number of nights equal to Protean. Upon losing humanity, they must check for physical degeneration or else permanently gain a bestial feature. These features can be temporarily removed through use of protean, but generally return after a scene.
Tismanu - Thaumaturgy
Primary: Sigil. Thaumaturgy creates a metaphysical bond between master and pupil equivalent to the Blood Bond, though it doesn't replace the blood bond. For Tismanu, the Sire always counts as the teacher. For others, the initial teacher counts, though he gains a level 1 bond to any subsequent teachers.
Secondary: As the Assamite Sorceror Disadvantage. (possibly reverse these)
Bloodlines
Clan defines the character's primary Discipline and weaknesses. Typically, a character may choose one Physical discipline as part of his personal repertoire as well as one other discipline, which may be another physical discipline, or one of the remaining six disciplines. This is where bloodlines come in. Bloodlines are established lineages that bear consistent disciplines.
Major Bloodlines here are equivalent to Clans of Masquerade, and Minor Bloodlines equivalent to Bloodlines in Masquerade. Each of these bears the cultural associations normally found in the Masquerade version, but are in certain ways acknowledged to be of the same overarching clan. It is also known that certain minor bloodlines came from certain major bloodlines, while others arose independently.
There may also be minor Lineages, which are essentially player or storyteller created bloodlines that have continuity. These may exist within a Major or Minor Bloodline, in which case they have the same properties as that bloodline and are simply a role-playing tool, or they may exist outside known Bloodlines, but have their own continuity of Disciplines. These lineages will likely be looked down upon relative to members of established bloodlines.
Last of all are Caitiff, who still belong to a clan, and may or may not have been spawned by a particular lineage or Bloodline, but for some reason don't carry the traditional disciplines of that lineage. Though they may still claim a clan, and possibly their parent bloodline may speak for them politically, they are generally considered mongrels. It should be noted that there are several lineages in different clans that are lineages in the sense of sire/childe relationships, and that don't carry disciplines from generation to generation, but nonetheless maintain a cultural/political continuity. The Panders could be regarded as one such lineage.
To-Do about Bloodlines
Since there are no specialty disciplines, Clans and Bloodlines that bear such from Masquerade will instead have standard disciplines with some additional Devotions set to replace and/or emulate all or part of those specialty disciplines. These will generally be somewhat proprietary to those bloodlines. Where possible, these will be drawn from existing Devotions and Discipline powers (preferably from requiem, though hybridized where necessary). Additionally, I may implement bloodline weaknesses and advantages, as an added incentive. In this case, I may cut down the Clan/Discipline weaknesses and use the other Weaknesses for particular Bloodlines.
OK, found the entry on this topic I had already written. Here it is below. Consider both segments. They vary somewhat in details. I'll more likely go with the naming system below, but I went into more details about some things above and a little more technical below. I'll reconcile those at some point.
Bloodlines
Clans are defined on the basis of intuitive mastery of a particular discipline and the natural side effects of this. The Seven Disciplines are divided into roughly three categories, psychic, which involve affecting the minds of others by extending one's own mental presence in some way, physical, involving manipulating the kindred's body in some way, and psychokinetic, which involves extending the kindred's psychokinetic power over his own body to the surrounding environment. Also, a mix of these methods. Upon transformation, a Kindred intuitively grasps the opening abilities of his own clan's Discipline, one of the physical Disciplines, and one other Discipline (which could be another physical Discipline).
So apart from Clan Discipline, a player chooses (i.e. the character's proclivities determine) what other disciplines he has. So each Clan has 24 (3 x 8) (168 total) variations, all of which will appear at some time or another. In this context, a bloodline can simply refer to a lineage, though sometimes it refers to a lineage in which the bloodline founder's choices overbear those of his descendants, in which case they simply all have the same set of disciplines and flaws. Physiologically and Supernaturally, this doesn't distinguish members of the bloodline from other members of the Clan who happen to have the same combination of Disciplines, however, historically and socially, a bloodline may have the advantage of solidarity and a similar mindset, and offspring of the lineage that cease exhibiting those characteristics, whether from distance or from the individuals own strength, tend not to be treated as members of that bloodline, though they are still members of the same clan.
Clan in this sense is treated much as Clans in Requiem are treated, essentially as the broadest form of relationship.
However, Bloodlines are more like Clans from Masquerade, and several of the Masquerade Clans are here represented as bloodlines.
Bloodlines are a matter of both lineage and culture, and generally only one of that lineage who also participates in the culture of that Bloodline will be considered a member. In rare instances, an individual of the same clan that has the same Discipline set and also forms a close alliance with members of the bloodline might be inducted into it. Typically members of other clans with the same discipline set will not be, nor will individuals with significantly difference discipline sets.
(Still Considering whether or not bloodlines have specific advantages/disadvantages)
Nergal - Animalism
Nosferatu - Animalism, Obtenebration, Potence
Brujah - Animalism, Protean, Potence (Lost Boys style Brujah)
Malakh - Auspex
Malkav Auspex Dominate Obtenebration
Ashur (Cappadocian) - Auspex, Fortitude, Thaumaturgy
Tismanu (Salubri) - Auspex, Majesty, Fortitude
Veddartha - Dominate
Annanaku - Dominate Animalism Fortitude (i.e. Requiem style Ventrue)
Tzimisce - Dominate Animalism Auspex (Old Clan Tzimisce)
Daeva - Majesty
Arikel - Majesty, Auspex, Celerity
Ilyes - Majesty, Celerity, Potence (replacement for True Brujah)
Ventrue - Majesty, Dominate, Fortitude
Khaibit - Obtenebration
Mekhet - Tenebrus, Auspex, Celerity
Lasombra - Tenebrus, Dominate, Potence
Sutekh - Tenebrus, Majesty, Protean
Ennoia - Protean
Andeleon (Tzimisce) - Protean, Auspex Animalism ("New" Clan Tzimisce
Gangrel - Protean, Animalism, Fortitude
Barjot (City Gangrel) - Protean, Obtenebration, Celerity
Vedma - Thaumaturgy
Tremere - Thaumaturgy, Auspex, Dominate
Koldun - Thaumaturgy, Auspex, Animalism