Hi!
There are some different opinions about base defence around. I´d like to add my opinion, too.
I think the most important thing is to keep the scenario believable. And this is difficult. Phalanx is supposed to be a professional elite organisation, if their architects would design an underground lair, they would certainly spend a lot of time thinking about handling invasion attempts. In fact, the art of building effective defence structures is ancient, from celtic pile defences over medieval castles to modern nuclear bunkers - they all follow the very same principle: Giving the defender as much advantage in defending as possible by design!
For a nuclear bunker, this usually means its an underground lair, deep inside a mountain. Depending on the depth, they would resist more or less intense nuclear attacks. If you assume there could be invasion attempts, you have to design the entrance part carefully, since this is the weak point of your facility. The good news is, if you are deep inside a mountain, you have a long tunnel which is easy to defend.
Typically such a tunnel has a branching after a few hundred meters. If you go straight ahead, you will find a dead end. This is where missiles are misleaded to, they wouldn't cause any harm, their detonation would blow through the tunnel like through a gigantic cannon, some dead guards, who cares as long as the lair is unaffected?
This pattern might be repeated several times with slightly variations. After the first or second branch-off the dead end wouldn't be just dead, but deadly: there would be an emplacement of some gatlings for example. I don't mean an infantery weapon - lets talk about the GAU-8/A Avenger! Imagine four of them behind a huge block of concrete with small holes to fire through. Well, now imagine the operators inside the bunker recognize an intruder approaching through the tunnel. They press a trigger and the Avengers fire a burst for exactly one second! Result: The intruder experience 280 incoming rounds with around 1 km/sec speed and a weight of 400 gr each. Honestly, I don't want to be member of an intrusion squad in this situation! There is no cover in a tunnel made out of concrete, and you still have to go some hundred meters fo the next branch-off. Even a tank wouldn't withstand such a burst, and nobody prevents the operators from pushing the button for another 5 seconds..
This obviously applies just to facilities which are independent from direct ground access. Of course you cant protect a hangar like this. But in my understanding most UFO:AI base facilities are protected like this. HQ, powerplant, hospital, R&D, workshops etc are placed in such a bunker and hence inaccessible for any intruder. Or the other way round, if an intruder has the power to cope with those defence mechnisms, then its pointless to try hunting him down with infantery weapons.
So, if UFO:AI has missions with intruders in such areas, there should be an explaination how it came to that situation. Teleporters or cloaking devices are possible solutions, though I am aware of the story impact. Or they were brought in hidden inside a container - those bastards!
Looking forward to your opinions/additions,
Pirx