TRIBAL AFFILIATION
Similar to Hindu castes, these would be hereditary traits granting small bonuses. While Judaism itself is considered to be maternal, tribal affiliation is typically handed down from the paternal line. This has potential to be different through matri-marriage perhaps, but that issue isn't really addressed AFAIK. In the Middle Ages, despite there being some supposed 10 lost tribes, around half of the total number of tribes was commonly accepted to lie within certain groups. Since there are only a handful of Israelites at the start of the game, and the powerful Ethiopian rulers have their status well-documented, it would be a matter of minimal designation and a lot of randomized trait-giving whenever a Jew is spawned.
Judahite: The main population of Jews, the Judahites descend from the Tribe of Judah from which the word "Jew" is derived. This might be considered equivalent to the Kshatriya caste for gameplay purposes, in that the majority of characters will fall into it and it should grant a level of prestige. The Judahites are traditionally said to be the tribe destined for kingship. They're the tribe from which the Line of David was birthed, and from which the rumored Messiah is to come from. It seems a little tick of prestige would thus make the most sense, not least of which because it's the Jewish standard. Adding an additional diplomacy stat boost might also be warranted. The Solomonid kings should be given the Judahite trait, regardless of their Christian status, just like how one does not lose Kshatriya for converting away from Hinduism.
Levite: Representing the most holy of tribes, the Levites are the descendants of Levi, and by extension of Moses, Aaron, and many priestly figures. Indeed, the Levites are the priestly tribe, the most educated of Israel. Their status as the learned urban leaders of the tribes even led to the other tribes paying them a tithe. Suffice to say, this is essentially the Brahmin caste. Levites should get a piety boost equivalent to that of Judahites. Adding a learning bonus equivalent to the proposed Judahite diplomacy bonus would likewise follow. The House of Gideon, rulers of the Kingdom of Semien, should be Levites. This tribe is the only one that both Jews and Samaritans should be able to spawn as.
Simeonite: A bit more contentious are the Simeonites. While many would say today that they've fully blended and integrated into the Judahites, in the Middle Ages the Simeonites were still recognized as a distinct tribal entity. In antiquity, the Simeonites were well known for being violent and brutal warriors alongside seeming to be mostly shepherds far later in history than any other tribe. This legacy carries over into the Middle Ages, where Eldad haDani lists them as a great and powerful tribe, and connects them to the mighty Khazars. Khazar leaders don't necessarily need to be assigned to a tribe, though. With this in light, and with their hardy origins, the Simeonites would make sense to get a small boost to martial stat, and in lieu of a ticking bonus to instead likewise get a small bonus to health. Speaking of Eldad...
Danite: The Danites, generally considered one of the lost tribes, had a new home in Ethiopia. The Beta Israel have claimed lineage from the Danites for millennia, which is ironic because none of the Ethiopian leadership in CK2 would be Danites. Now, these guys seem well-suited to be a merchant republic. They were traditionally said to be seafarers, some of the only among Israel, and later would be associated with scales. Scales of justice, but still scales! More firmly, however, Eldad says that the Danites settled in the "land of gold". Call it a stretch but these might be our Vaishya, with a small income bonus and perhaps a stewardship bonus as well in accordance both with mercantile habit and with their association with justice.
Benjaminite: These pugnacious fellows are the first of three Samaritan tribes that we shall discuss. Just as Jews may spawn with the four above, and if possible Ethiopians may be slanted towards being Danites, characters of Samaritan religion will spawn as one of these upcoming four or as Levites. The Benjaminites are recorded as being fearsome, and strategic. The Benjaminites learned to fight left-handed, that they may surprise and defeat their enemies. Their blessing from Jacob indicates a life of constant fighting, day and night. To me, this seems to point clearly to a mixture of martial and intrigue, perhaps getting a smaller bonus to both as compared to the larger singular boni given to Jewish tribes. They're also famed archers, and might get a boost to leadership accordingly.
Ephraimite: The second of the Samaritan tribes, and the first of the Josephites, the Ephraimites have a long history of rivalry with their closest kin, the Manassehites. Favored by Jacob, despite being the younger of the two brothers, Ephraim was known as a modest and pious leader. The tribe of Ephraim would essentially be the equivalent to the Judahites for the Northern kingdom, and accordingly their boni will likely be quite similar. With these all in mind, I'd say their boni should be diplomatically focused, but without extra prestige such as Judah has. They should get a negative "Sibling Rivalry" opinion modifier for people with the Manassehite trait, as one of the half-tribes of Joseph. A penalty with Judahites might be considered for their ancient rivalry in the North vs. South struggle, but is not really that important.
Manassehite: Another tribe of warriors, the tribe of Manasseh was famed for exploits like the Shibboleth Incident, warring with Amorites, and according to Eldad haDani they were born and bred in the saddle- he associated one half of the half-tribe as being among Khazars and the other half as being cavalry warriors wherever else they roamed. The Samaritans may have a disagreement with this, but the tribal history still leads us to a conclusion of high mobility- their land was not only the widest of all the tribes, but was also filled with valleys into which roads were built. In legendary wars, the tribe of Manasseh was said to supply excellent scouts, building onto their legacy of swiftness. This is the most purely martial of the Samaritan tribes, and should accordingly get a sizable martial bonus. Perhaps a cavalry leadership bonus or a movement speed bonus on top of that. Tack on the "Sibling Rivalry" malus with the Ephraimites and you've got yourself a deal.
Issacharite: Finally, a Samaritan tribe that isn't warlike. It's funny how much they stack up. Anyways, Issachar is considered a scholarly equivalent to Levi, though not blessed with priestly status. Just as Simeonites and Levites are the swords of faith, the Issacharites and Levites are the scholars. It was said that there was not a scholar in all Israel who was not one of these two. While the Levites are dedicated to strictly theological and artistic endeavor, acting as musicians, priests, and guards of the holy places, the Issacharites instead became embroiled in legal study alongside religious study. Associated in their blessing by Jacob with abundance, industriousness, and piety. Eldad haDani insists the Issacharites he met lived under the rule of a judge, and all lived by the laws of the holy texts in accordance with the letter of the law. With all of this blending of faith and legalism, as well as abundance and industriousness, it is safe to say the Issacharites should get a mixed learning and stewardship bonus, perhaps through stat boosts or perhaps through minor piety and income bonuses.
BLOODLINES
Kohenic Line: The Kohanim are the direct descendants of Aaron, the first High Priest of Israel, and the brother of Moses. All Kohanim are Levites, but not all Levites are Kohanim. They are the priestly caste of the priestly tribe. Characters generated as Levites should have a small chance to spawn with a Kohenic bloodline. Only Kohanim should be allowed to become the Kohen Gadol when the Third Temple is built. By the Middle Ages, the last known custom for appointing a High Priest was through civil authorities. In this case, I would suggest that a College of Cardinals type deal could be set up with potential candidates, including the player if they hold the bloodline, and various factors to automatically elect the next High Priest. Alternatively, the acting King of Israel could appoint successors by hand similar to appointing a bishop. This bloodline is patrilineal.
Holding the Kohenic Line should provide the player with a sizable religious authority bonus, piety per month, and a learning bonus. The Gideons in Semien should hold this bloodline.
Davidic Line: Descended from King David of Israel, the Davidic Line is truly legendary. A few notable individuals of the bloodline appeared all throughout the Jewish world in the Middle Ages, demonstrating that it was so important that such things could still be kept track of millennia after the fall of Israel itself. The House of David was blessed with kingship in the past, and is destined for it once more. The upcoming eventual Messiah is required to be of the Davidic Line, though that is the Messiah, not necessarily a Messiah like Cyrus the Great, or whatever character might restore Israel. Interestingly, this is actually a cognatic bloodline- while it passed from father-to-son in the days of the monarchy, Sanhedrin members in later history claimed the Davidic Line through a matrilineal inheritance via Hillel. Ergo, it should be passable through both son and daughter. Although traditionally associated with the tribe of Judah, the Davidic Line's cognatic inheritance means that it can easily pass into other tribes as well. Even still, it should be an exceedingly rare trait in Judahite courtiers alone if we go by people generated by "invite X" decisions.
Holding the Davidic Line should provide a sizable learning and diplomacy bonus, prestige per month, and a possible vassal opinion bonus. The Solomonids in Abyssinia are the only dynasty that should start with this bloodline.
Messianic Line: Invented when Israel is restored and the Third Temple is built, this bloodline is founded by the King or Queen of Israel when both conditions are met. Similar so Saoshyant, Sayyid, or Augustus, it will stick with your family for a very long time. I'll be honest, this would basically be a reskinned Saoshyant (descendant) and that's honestly just fine. I think the bonuses here are really self-explanatory and could just be direct copies of the Saoshyant (descendant) bonuses.