One thing I notice in these discussions is a focus on the "genetics" or physicality of lineages, which is kind of illogic since they are made up and don't actually have a genetic history.
I think it's a much better idea to build a ruleset off of the "narrative truths" of each lineage. What should it feel like playing as an elf vs a dwarf? What rules support that playstyle? I think freeing ability bonuses from races gives future designers to focus on other abilities, proficiencies, and powers that give each lineage a unique feeling no matter your ability scores.
If it were up to me, I'd break it down into three parts.
Your lineage grants you unique proficiencies, powers, and narrative truths that help, say, and elf fighter and an elf wizard feel like they are playing the same lineage. There would be no ability bonuses for lineages.
There would be a +1 bonus to an ability scores through your background, though these could also be presented as a choice. As a character with a noble background, you can choose +1 to Charisma or Intelligence.
The +2 would come from class. It just makes sense to gain a +2 to Dexterity from your training to become a rogue.
Just like background and class skill proficiencies, if your background and class ability bonuses are the same you just choose a new one.
As for lineage powers, I would follow a thought pattern like this:
When I play as an elf, I want to be a bit otherworldly. So whatever bonuses I get should make me feel like a magical race that doesn't follow the same natural laws as humans.
Elf:
Sleepless: trance instead of sleep for 4 hours a night, immune to sleep spell effects.
Otherworldly sight: choose proficiency in two skills (Insight, Investigation, Perception, or Survival).
Then I would have some lineage feats or powers associated with different ideas of what it means to be an elf. Say, something like...
Elven Weapon Proficiency: you gain proficiency in short swords, longswords, shortbows and longbows.
Inherent Magic: Gain access to a cantrips from the Wizard spell list.
As part of choosing your lineage, you choose one lineage feat from your lineage or another's.
Anyways, that's how I'd do it!