Separate lineages into classes, defined by colored borders, and given different chances of rolling them by adding multiples of lower classes, in addition to there simply being outright more of lower classes than higher classes.
Green: Four entries (Meaning a Green lineage would have three results/clones of it, increasing chances.) In addition to there simply being more Greens than Yellows.
Yellow: Three entries, in addition to there being more yellows than oranges.
Orange: Two entries, in addition to there being more orange than red.
Red: One entry (per lineage)
EXAMPLE (Colors only. The lineages displayed may or may not fit into the color given to it for demonstration purposes):
Additionally I'd recommend a single Blank entry per class, in which the player may come up with their own custom color/class-appropriate lineage. A Red custom would still not be comparable to a Sacred lineage, but a single golden lineage result could result in a Custom Lineage scroll. Meanwhile there could be a simple silver one that lets you make a custom Red lineage (rather than having one custom per color).
Some basic suggested guides:
Green: Lineages that provide some simple standard effect that doesn't scale. Such as perhaps a spell that lets you change colors of things temporarily/chameleon yourself.
Yellow: Lineages that provide some combat effective utility such as the ability to teleport x meters every other post or so on, or something like the Truth lineage's Anti-magic AoE.
Orange: Lineages that can be an obvious trump card / change how your combat style works / magic works. Such as Archmage's ability to alter your magic's elemental properties. Or a lineage that lets you reverse magical and physical effectiveness or offensive and defensive effectiveness.
Red: Lineages that have user-ranked effects, scaling as you grow. Such as the ability to project a user-ranked fireball, or control nearby water with user-ranked strength. They might also grant a free ship, as ships have user-ranked functions.