In terms of chronology, Metroid Prime 2: Echoes is the fourth game in the Metroid saga. It is chronologically preceded by Metroid (Zero Mission), Metroid Prime and Metroid Prime Hunters. It is followed by Metroid Prime 3: Corruption, Metroid II: Return of Samus, Super Metroid, Metroid: Other M and Metroid Fusion.
In the beginning of the game, one of the Luminoth Lore data files (History - Golden Age - Origins) describes how the Luminoth travelled through the Galaxy and came into contact with several enlightened species, amongst others the Chozo. In the instruction booklet of Metroid Prime, it was told that the Chozo shared their technology freely with several other less-developed species. So the most logical explanation would be that part of Luminoth technology is derived from or strongly inspired by Chozo technology, and therefore compatible with Samus' Chozo technology.
What could make this theory sound more plausible may be a further understanding of how Samus' suit works. The ending of Metroid Prime 2: Echoes already explicitly showed that the suit is not a traditional armor that needs to be disassembled manually: its solid parts can materialize in and out of existence. From Metroid Fusion, Metroid: Zero Mission and Metroid: Other M it became clear that the blue Zero Suit that Samus wears beneath the metal is the interface that Samus uses to activate the solid exterior armor; it is strongly affected by Samus' emotional state (the metal can glitch under duress), and vice versa, when the armor takes hits, it also affects Samus since she reacts in pain. So this may mean that every suit upgrade, even though often represented by an object, is, in fact, data that the Zero Suit can read, interpret and integrate into the armor. Think of it as software that is uploaded into the suit, so it can be modified to produce new functions. It isn't too far-fetched to assume that Luminoth data is either compatible with Chozo hardware, or that the suit can translate the data to make use of its upgrades.
What could make this theory sound more plausible may be a further understanding of how Samus' suit works. The ending of Metroid Prime 2: Echoes already explicitly showed that the suit is not a traditional armor that needs to be disassembled manually: its solid parts can materialize in and out of existence. From Metroid Fusion, Metroid: Zero Mission and Metroid: Other M it became clear that the blue Zero Suit that Samus wears beneath the metal is the interface that Samus uses to activate the solid exterior armor; it is strongly affected by Samus' emotional state (the metal can glitch under duress), and vice versa, when the armor takes hits, it also affects Samus since she reacts in pain. So this may mean that every suit upgrade, even though often represented by an object, is, in fact, data that the Zero Suit can read, interpret and integrate into the armor. Think of it as software that is uploaded into the suit, so it can be modified to produce new functions. It isn't too far-fetched to assume that Luminoth data is either compatible with Chozo hardware, or that the suit can translate the data to make use of its upgrades.
Aether is described as a planet with unstable planetary energy. This is probably what causes the 'atmospheric interference' mentioned by one of the Marine Troopers, and what caused the Marine's and Samus' ships to malfunction.
Perhaps the combination of this atmospheric anomaly and the semi-sentient nature of the Phazon in the object are responsible for the disappearance of the stellar object/meteorite that hit Aether, and the creation of Dark Aether. An impacting meteorite has tremendous amounts of kinetic energy. Maybe the mass and energy of the object were (partially) absorbed by the atmosphere; this provided the energy for the dimensional schism that duplicated Aether and created a twin world. The twisted nature of the Phazon present in the meteorite probably caused this planet to be Phazon-based, which would acount for the dark nature of this twin world, and the creation of the Ing. A same sort of thing happened when Samus defeated the Metroid Prime in Metroid Prime; the Phazon blob sampled her and her suit and created a Phazon-based (thus 'dark') copy.
Perhaps the combination of this atmospheric anomaly and the semi-sentient nature of the Phazon in the object are responsible for the disappearance of the stellar object/meteorite that hit Aether, and the creation of Dark Aether. An impacting meteorite has tremendous amounts of kinetic energy. Maybe the mass and energy of the object were (partially) absorbed by the atmosphere; this provided the energy for the dimensional schism that duplicated Aether and created a twin world. The twisted nature of the Phazon present in the meteorite probably caused this planet to be Phazon-based, which would acount for the dark nature of this twin world, and the creation of the Ing. A same sort of thing happened when Samus defeated the Metroid Prime in Metroid Prime; the Phazon blob sampled her and her suit and created a Phazon-based (thus 'dark') copy.
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