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I am worried about the possible plot hole in all the Mass Effect universe, namely about the planetary defense systems. It is true that both Sovereign (and Saren, its agent), and the Collectors later on, attacked only rim planets, colonies largely undefended. It is also true that, on side missions, Shepard largely landed on planets used for guerilla operations by mercs. But two things bother me. The first is the apparent lack of surface based defense system on the Citadel. The second is the clear and present reluctance of the colonies to install planetary defense system, as portrayed in ME2's Horizon.
It is improbable that a space station with such sophistication and importance like the Citadel lacks surface based defenses. The Council had experienced wars with the rachni, and later with the krogan, to know well enough that losing a war is not an impossibility. In fact, they were losing the war with the rachni when the salarians decided to uplift the krogans. Then they were losing the war with the krogans when the turians deployed the salarian-invented genophage against the krogans. Indeed their fleet is mighty. But it a folly to think that no adversary can reach the Citadel itself. Militarily, the seat of power would be the best garrisoned and defended habitat for all sentient races. The Citadel is indeed the best garrisoned. Destiny Ascension was the best dreadnought in the entire fleet (and stil is if Shepard decided to save it). They have tens of turian warships of the cruiser class. But it's surface based defense system is wanting. There apparently is no surface based turret, e.g. of the GARDIAN class, on the Citadel. True enough, the Citadel can close like a clam in case of invasion. But no clam can withstand pounding. There should be, at the very least, GARDIAN turrets in the outer surfaces and kinetic based turrets in the inner surface of the Citadel, in case of the enemy breaking through the outer defenses. We do know that one GARDIAN turret on the Horizon can force a hasty retreat of a Collector ship (which is probably of the dreadnought class considering the size, though the game calls it a cruiser). An array of GARDIAN turrets should be able to deplete the shield of any Reaper to enable the defending fleet to destroy it.
Better still, the Citadel should have an array of off-surface (i.e. space based) defense system. Like space platforms for kinetic missiles or laser turrets. This array could act as the first line of defense against invasion before the fleet can move into defensive formation, or as support fire for the defending fleet.
True enough, the turians were shocked in the First Contact War because they didn't expect a forray deep into their defenses as a viable war strategy. Humans prevail in the Council because their tactics are superior to other races. But still, how come an intelligently superior race like the asari, or the military based race like the turian, fail to see the necessity to install surface based defense system?
The reaction of Delan on the Horizon underlines the fact that surface-based defenses aren't welcome. He grumbled about the instalment of a single GARDIAN turret is enough to provoke invasion. Thus, to avoid invasion, an outer colony should not install any defense whatsoever. What a confused thinking! Since when an undefended location is better protected against invasion than the defended ones? If the GARDIAN had been operational in the first place, the Collector ship couldn't have landed on the planet, don't you think? Ahsley/Kaidan was on surface and survived the attack. Thus the Alliance should have the knowledge how to prevent further attacks -- install GARDIAN arrays, make armored bunker as the targeting command quarter, and equip security officers with armors such as the one Ashley/Kaidan was wearing. Though that armor could not prevent being immobilized by seeker swarms' sting, they wouldn't be permanently immobilized.
Shepard said something interesting before the final battle in ME2, "The Collectors blindside their target... they hit and run." At one moment I realized that this is precisely what the Reapers do. They activate the keepers, open a mass relay within the Citadel and strike without warning. Right into the heart of the defense, not unlike a Trojan Horse. That way, any defense would be futile, space- or surface-based. But now the Council has experienced an attack that cut through the Citadel's defense like a hot knife cuts through butter. It will be a massive folly if the Council let the turians build more cruisers or dreadnoughts (like what the galactic news keep repeating) instead of focusing on building defensive parameter around the Citadel. The races have the tech: the Thanix cannon is really a bad-ass. Install them around the Citadel. And it might be the last march for the Reaper if they try a frontal attack against the Citadel.