...that's not really a compromise.
I want it to scale.
Then I'd suggest the following modifications :
Lord Above
This ability greatly increases the size of the Swarmlord. She increases by one size category, gaining +4 Str, +4 Con, -2 Dex and the standard size based changes to attack and skill rolls. These ability scores are instead of the usual changes to ability scores.
This is better than the Size Change swarmling evolution. I'd suggest to make the benefits the same than 3 points in Size Change. This would also allow you a Size Reducted swarm.
Sky Swarm
This ability grants a Swarmlord great wings, or some other means of aerial propulsion. She gains a flight speed of 30ft (Average), +10ft for each five levels she possesses, and increasing in manoeuvrability by one stage for each ten levels she possesses.
Suggested rewording (the benefit for the swarm doesn't change) :
Spoiler
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Sky Swarm
This ability grants a Swarmlord great wings, or some other means of aerial propulsion. She gains a flight speed which depends of her swarmlord level :
Level | Flight speed | Manoeuvrability
4-9 | 30 ft. | Average
10-14 | 40 ft. | Good
15-19 | 50 ft. | Good
20 | 60 ft. | Perfect
The flight speed and manoeuvrability doesn't increase after the 20th level.

Weapons of the Queen
This ability grants vastly improved weapons to the Queen. She may gain an additional natural weapon for each five levels she possesses, and she may grant an enhancement bonus to each of her weapons equal to a third of her class level. Points of enhancement bonus may be traded for special abilities, and the enhancement bonus may not surpass 5.

Taking this ability gives each Swarmling she possesses up to two free points in the Additional/Enhanced Natural Weapon evolution, which don’t count towards their cap.
Suggested rewording (then again, swarm's benefit doesn't change) :
Spoiler
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Weapons of the Queen
This ability grants vastly improved weapons to the Queen. She gains an effective enhancement bonus to her natural weapons equal to one third of her level (rounded down). This bonus can be spend on weapon properties, but the real enhancement bonus can't exceed +5. She also gain more natural weapons, as with the Blade of the Queen class feature, according to her level :
Level | Additional natural weapons
4-9 | 1
10-14 | 2
15-19 | 3
20 | 4
She doesn't gain more natural weapons after the 20th level.


About swarmling evolutions, I noted an apparent flaw in Size Change : due to the wording, the +1 to natural armor seem to stack with the increase in size. Is this intentional?

While it's odd, it's intended. They should have those specific scores. It's not their mind anymore.
Then why 10 Cha? How does the act of being a member of the swarm increase by +9 the Charisma of a zombie?