My biggest complaints about the lost sectors are:
1. They are marked on the map and easy to find.
2. The chest at the end has absolute crap, like tokens or completely useless armor/weapons.
Why would the fallen or hive give a damn about guarding tokens and gear they can’t use for any reason. They really could have been a very awesome side part to the game with great rewards.
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I don't really feel it would be as bad, being on the marked on map if they were actually difficult or long to complete . A more lore friendly solution would be to replace the tokens with various objects and knick-knacks of golden age tech and data or enemy resources you could exchange for gear , weapons and other stuff .