Preamble: It is sad, but the fact we have only one way to protect your base. For protecting you need the same squad as the enemy. Defense structures can not pursue the enemy, and therefore it is possible to systematically search for the key to the destruction of the base. The problem of linearity increases with the prime time.
That is: To protect the base, you need to have a strong defense squad 24/7. No matter how much effort you spent on the construction of the base. This is the only way. The current online is low, so the problem is not so evident. But when will start the wars 1000 vs 1000 it will become obvious.
It is stupid to try balance the game, modules, and the buildings for a different online. Personally, I think that it is necessary to implement a concept which does not depend on anything. The system should work with 10 ppl and over 9000 online.
For such realization we need to decide the approximate scenario of intrusion.
1) First invasion: The attackers should declare their intentions.
Of course the attackers will come to get some fun. But destroying of the whole base is unacceptable.
So there need the destroying some structures but the base should keep some defensive potentialities.
2) A little break. Defenders receive the signal that need to organize defense.
3) Big fight between attackers and defenders. If defenders wins then it's ok. If not - the next point.
4) In case of successful attack and destroying of the defense squad, it should be able to continue destroying of the base. But also should be able to protect the base with material/money (expensive).

Idea:
I ask for DeV's to remove stupid reinforcement.
Instead of reinforcement need to implement overload (enrage) and emission (peaceful) phases.
Overload:
After atack/destroying of the first building should be activated the alarm. In the same time starts activation of the overloading mode. Activation should take ~15-20 minutes. After that the buildings highly increases its resists, repairing, DPS, range etc (also maybe remained facilities and main terminal should activate turrets on its board). This phase should eat very high amount of energy.
After discharging of reactors and batteries the base should be able for next attacks. Of course should be able to prolong overloading phase with energy cells. This is nonlinearity factor. Even peaceful miners should have ability to def their base. With resources as well. (Else why need to mine?)
Also should be able to deactivate overloading mode (i think it should be able immediately).

Emission mode.
Nobody helped, defense squad destroyed, energy cells spent and so on. Intruders can to start the tasty phase - destroying the base.
1) Should be able to deconstruct some buildings.
2) Should remain facilities.
3) Should not be able to recreate defense system. The next and last battle for the base should be squad vs squad. Without defense buildings.

...That's why it called emission phase. After destroying defense/repair/buff/relay systems the players will be able to atack main terminal. But instead of reinforcement (imho) should start huge emision of interference with radius 2-3 km. In the emision zone will be impossible to lock anything. Also i liked the buff from the arena: discharging of accumulators.
During the emision will be impossible neither atacks nor mining/building/terraform etc. Only hauling and artifact searching.

P.S. I'm sorry for my bad English. I hope that you will try to understand my point. Here are no my interest to shift balance for my benefit.

TL;DR: There is no tl;dr. If you too lazy to read - it's better to leave this post.