Currently with the "New enemies" it tends to just pick a faction or factions and then make a lot of those.

What I would like to see is, it always spawns Normal biter bases for the majority of enemies. Then add some random sprinkles of special "New Enemies". That way you get a solid experience with some special surprises.

That way the player has the choice of going and killing the "Special" mobs nests if they don't want to deal with them. For example: Fire spitters are terrible, I would go hunting just for them.

Additionally, is there a way to reduce frequency of sieges?

Only 2 factions: "acid", "normal" at 0 - 0.15 evo. 8+ factions at 0.15+ evo. Just wait
0 - 0.1 evo - the "nursery" mode. To give the player a chance. After 0.6 evo, factions are significantly stronger than the standard ones

Sieges occur in 2 cases:
1. A lot of nests away and no/few near - AI creates the basis for attacks.
2. A lot of nests are close, the AI gathers forces to break through the entrenched player.
The key to the remaining sieges is a moderate number of nests.

In addition, the "migration" is a very "hard" parameter - it greatly increases the settlement of bitters (including sieges). It is disabled by default, because in fact it is a survival mode.

according to the tests on the sent save:
increased the threshold for triggering the "finishing" mode, since the included migration and sieges have already provided a sufficient base... base was eaten after half an hour of inactivity.

I recommend unchecking "migration". The b&a is slow, it will not keep up with the development of the enemy...

"That way the player has the choice of going and killing the "Special" mobs nests if they don't want to deal with them. For example: Fire spitters are terrible, I would go hunting just for them":

The bases have their own genome. So, if the fire gene is there, then fire nests will appear from existing ones.
The genome can mutate and this gene will disappear by itself. In addition, when a new Tier-level is reached, new set of factions will be applied. But it is not a fact that, for example, T4 is a "Physical" faction with a huge phys. resistance will be nicer than the T3 fire, which is killed simply.
Summary - if dont want specific gene, you need to kill all nests at enemy base, or wait for mutation.
But the idea of "player selection" is interesting.

Also, the main goal of the fire faction is to force the player to add lasers to their defense.
Fire spitters have weak damage, but perhaps it's worth making their appearance even later? (now they are tier3 = 27% evo if no handicap)