Cryptic could get around the loot issue, which is a pain in cruisers and i'm sure all other ships, by allowing you to beam the stuff into your cargobay or tractor it from 10Km. As it stands, the transporters are seriously bad. you can beam from almost anywhere when ur in a team down to a planets surface, even beam to someones bridge across the other side of the quadrant.
Simple, Scanner tells you what loot has dropped, you chose to beam or not to beam. More unstable items you cant beam as it is too risky, so you can send out a shuttle to retrieve it or lock on a tractor beam.
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