I don't know that there are any balance issues, per se, other than some races have other abilities that may be considered at the same "point value" as an ASI.
The real reason for racial bonuses is to reinforce racial stereotypes/archetypes. I prefer to have those archetypes in place, but it's not something that would put me out too far to have removed. If you're going to remove them, though, I'd just remove them for everyone, including humans (use the variant, sans ability bonuses). If that ends up making characters that are lower powered than you like, use a higher point-buy pool.
If you're using dice, then 4d6, drop lowest should work (it did in 1E). If that's too low, try 5d6, drop 2. If that's too high, then, yeah, a +1/+2 should do the trick. I just like keeping points and dice separate.