So some friends and I have been playing a heavily modded save for awhile.
Having gotten used to using Natural Evolution Enemies, which is now broken (yes there is another patched version of it, but it doesn't seem to want to spawn it's bases in new generated chunks), I've come to the conclusion the next best thing is probably the new enemies from Rampant. But, I got some ideas coming over here from there, and just wanted to throw up some ideas. Not that NEE had these features, just different mechanics, that inspired this.
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So my first recommendation is an option to disable the spawning of the "common" enemies. Allowing for all the enemies to be more interesting. I'm not sure if this will cause any issues with Bob's Enemies and the artifact drops, but not everyone is running that anyways, and you could experience the same issue if you were to disable all the enemies that drop blue artifacts.
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A variable in the settings to change how frequent the enemies change types. As of now they change types rather slowly, though perhaps faster the farther out they get. But compared to a lot of other mods, they are almost whole biomes of a single type, instead of a more mixed variety. I'm not saying you need to change the default by any means, but a scaler tagged on whatever equation you have to set how often they change might be a neat thing to have to allow people to make a more rainbow of enemies.
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In the same vein of the 2nd one, but probably more complex to implement (I don't know the Factorio API, or how your mod is put together). Variables to determine frequency of each type of enemy. This could even be a catch all for if they spawn or not, no check box needed. So I might decide to throw up a heavier weight for Inferno biters or some nonsense, so most of the enemies are that type.
Just some ideas, the first two of which seem like they would be fairly easy to implement.
Thanks for the great mod