Yea, but that’s because they don’t generate enough reinforcements to make it an interesting threat.
It’s a delicate balance, I know, but if there were enough enemies to keep you on your toes, evac’ing your squad from a Lair full of pissed off Pandas would be a tense, interesting exercise rather than a jaunty stroll across an empty map.
Imagine if achieving the goal would spawn an enemy on every spawn point… Still somewhat abusable (achieve the goal while being the closest possible place to the evac, f.e. using delayed damage [bleeding/etc., sacrificing a turret], trying to snipe it across the map, using a MCd enemy, or something else), but at least would make the “second half” of the mission actually… a mission?
IMHO this would look artificial and illogical.
If there were numerous enemy reinforcements at hand why didn’t they come earlier to prevent you from achieving your mission goal?
Having enemy rushing in to “avenge” the dead leader feels way less artificial and illogical than somehow teleporting out while surrounded by enemies on all sides when you achieve some “goal”.
Don’t forget, destroying 2 sentinels somehow means all the enemies self-destruct in a safe way and Haven soldiers give up and walk away when their most important air vehicle was not theirs for X turns (you can be on the other side of the map and still “leave with it”)…
I see especially Liars and Citadels as a form of infiltration mission to the central part of a bigger structure with only one goal, kill the boss in this part of the structure. Killing it would alarm (mentally, loud psychic scream, what ever) the whole rest of the Lair/Citadel and they will be pretty angry about what you’ve done.
I imagine angry bodyguards rushing into White House after you kill a president.
“We thought you wouldn’t do that. Now you’re toast!” 
If anything killing their mental leader would disorient Pandorans, because they usually receive telepathic guidance from them. That could justify ending the nest missions after the Sentinels are gone.
As for stealing air vehicles… yes, that’s just game mechanic. However more often than not I have the map under control at the end of this mission, so it wouldn’t be hard to evacuate everybody, especially when we have a flying ship at hand. The other interesting question is: does the Haven have no air defenses to prevent the ship take off and flying away? Especially with Festering Skies DLC incoming with promised air combat.
It should be the same with Lairs and Citadels and even after the research pandoran citadels this is mentioned:
Killing the controlling Scylla will cause a cascade reaction that will effectively destroy all biomass in the entire Citadel, including all the creatures created from it.
So contrary to my statement above, I have to agree with you here.
Destruction of the “main generator” leads to de-energization of the adjacent network.
Perhaps gradual? Then, a suicidal attack of the remaining monsters is logical.
Edit
I will add from myself:
Then, the Citodel / Generator should have 2-3 more Lairs / Substations available (for the Lair - 2-3 Nests). Upon the destruction of which, we will weaken the effectiveness / Power of the Citodel (destruction of the Nests, weaken the adjoining Lair).
Hmmm, yes and no … from research / wiki about lairs:
Based on our observations, when several Pandoran Nests come in contact with each other, a dominant Nest assumes control of the others, entering its second level of development.
… and citadels:
Our research shows that when several Pandoran Lairs exist in one overlapping territory, they merge into one single structure.
I wanted to add on my own, continuing the logic of the Citodel = Network.
I find the logic of cutting roots very interesting. But it takes a creative approach to rebuilding Pandora’s Bases.
I would rather find it interesting when they would follow this logic also in the game itself. Once Lairs or Citadels introduced they can spawn directly without any underlying network of existing Nests / Lairs.
I assume they abstract it for a smoother gameplay.
Would they always start with only a Nest that had to join with two others etc then the player would have a easy way to hold them back when the research of the Citadel is done (<- detect Pandoran colonies in scanning rage).
I think that is left over from the old system where we scanned with the aircraft and not the bases. But I also don’t know if they followed the “corract” path before this change (3 nests -> lair, 3 lair -> citadel).
Similar thoughts.
What if you give the player a choice?
Direct attack on a strong Citadel or a chain of 2 missions: weak Lair + weak Citadel.
Edit:
The problem is that the Nest and Lair missions are the most boring right now. But there should be more of them, in that case.
Edit:
Variety of missions for the Nest and Lair:
As the most frequent / repeated missions.
This is in my experience already the case EDIT: I meant the amount of bases, more nests, lesser lairs, rare citadels.
And they “evolve” over time but independent from near other structures, nests → lairs → citadels and this sometimes pretty fast.
I just had that, a nest was detected and before I got there it had evolved into a lair.
Eh, those are the few missions where surprises can happen, so my favorite mission types. Quite different Citadel, always the same map (the small changes in details are not really noticeable and also do not matter)
If you combine thoughts from me and @MadSkunky, then Citodels will appear less often, but they will be much more difficult.
Updated above.
I try to put them a bit together, could be a longer post 
The idea that came out after some brainstorming via PM with @noStas:
If 3 Nests unite to form a new Lair, then the 2 weaker ones are abandoned and thus destroyed. Everything gathers in the largest Nest and a Lair is added to the existing Nest. The same then with 2 more Lairs within reach, where the 2 weakest are left again to build a Citadel, also additional on the remaining Lair.
Different structured layouts growing in size and variety, see also @noStas comment above.
In the end you have a more complex large structure made up of Nest-Lair-Citadel, all directly connected. The player can then decide to fight up from Nest to Citadel in single steps. These are then individual missions, the following can be completed after a minimum time, otherwise the Nest / Lair will be rebuilt. The destruction of the Nest weakens the Lair and so also the Citadel, the destruction of the Lair again weakens the citadel and then the last step should not be too difficult.
But, the player can also attack Lair or Citadel directly, of course much more difficult if the subordinate structure has not been destroyed.
Main raw concept of attacking such a structure see comment from @noStas above
This way such structures could grow independently on the whole globe, but not as much as currently and the player has to prepare longer for such a mission chain or the very difficult direct attack on the Citadel.
Some additional thoughts:
The immediate detection of all pandoran structures in scanning range with research of the Citadel has to be changed. Otherwise the player just has to destroy every spawned Nest to hold the Pandorans at low level without evolving to Sirens, Chirons, Scyllas. I would make the detection of low Nests really hard and increasing chances when the whole structure/net grows. Something like that …
Overall lesser haven attacks from smaller Nests, increasing when they grow, same with Lairs:
Giving the player more time and lowering the overall pace
The Nests are harder to detect in the early stage of the game when they don’t attack that often
The structure get the time to grow up to the Nest-Liar-Citadel
Any thoughts, additions, ideas?
Ok, but this would mean more citadel missions overall, because nests are hard to detect?
I would think even lesser Citadels, not more then 2 or 3 at once, maybe even hard capped to only 1 at once. And when you destroy Lairs (easier to detect) they have to evolve from scratch with 3 new Nests.
Edit:
The point is, with this system there are 9 Nests necessary to build the 3 Lairs that are necessary to build the Citadel. And even more of the Nest are scattered unconnected around to find each other. Even when a single one is hard to detect, it should not be hard to detect at least some of the many.
A picture to show how such a structure would grow up, the big arrow shows the 3 different possibilities to attack the final and biggest structure of a Nest, Lair and Citadel. All bases that are crossed out are abandoned after they have integrated/evolved into the next larger structure.:
Attacking direct the Citadel should be the most difficult mission if the Lair and Nest are still alive and so there are more enemies in, these subsequent structures can also send permanently reinforcements to the Citadel.
Attacking direct the Lair should also be difficult but not as much as the Citadel, also more enemies, reinforcement etc.
Attacking the Nest should be the easiest task with not much enemies and low reinforcements
Single Nests or Nest-Lair structures follow the same principle but should be even weaker.
This is a pretty big thing to thought about … omg 
Edit:
Just a little remark, the main goal for me is to reduce the amount of haven attacks overall and also the amount of Pandoran base attacks and make them less boring, more interesting, with more variety.
Nests should be weak and rarely attack Heavens and even then mostly will not be able to win the attack, Lairs a bit tougher but not that much. Their main job is build the above structure to evolve to a bigger threat. This should cost time and so reduces the general pace for the player.
Edit, part of the “battles fought” result page of my last campaign (ended at 27.03.2047 in game time):
68 missions with haven defenses and destroying pandoran bases, 30 HD and 24 Nests. IMHO way too much.
Feedback for this particular issue: Too much Haven defeses and Pandoran base attacks
The way Pandoran structures are currently generated is definitely problematic, because
it doesn’t fit the lore (2 Nests within each other operating range form Lair, while the Nests become abandonded, and same with 2 Lairs and Citadel),
Pandoran colonies that don’t have any havens to attack don’t do anything besides contributing to a hidden max cap, and
The whole thing is really governed by hidden counters telling when to spawn a new base or to launch an attack.
All this adds up to an unsatisfying feeling that the whole thing is just arbitrary.
And there is also this:
The @noStas and @MadSkunky idea is pretty good, imo
I like the Network Idea, a lot.
I dont feel adding difficulty or making the mission longuer would be a good idea, However, I can see an evac mission atached to the citadel, but It should be a distinct mission provide the player a resuply option or not require too much ammo. Also I dont think it would work unless a carry wounded soldier mechanic is implemented, which would fit a more runnaway than killing focuss (which would be hard to do) but would also fit the not requiring too much ammo.
