Yea. There's some gaps of logic here. I mean, our ship gets destroyed. We return to a station which doesn't even have a shipyard, but we get our complete ship replaced. Including the special one-of-a-kind engineering setup, which just was destroyed. We survive, but our crew member reliably failed to eject.
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Outside of logic, it's just some failed game design. Rebuy costs hurt, but only up to a certain point. So somebody decided that deaths should always hurt by killing your crew. Of course, "always" is only if you have active crew.
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Instead of the current nosense, I would suggest to actually make something useful out of this mess: gameplay. You can say that the crew members escape pod arrived somewhere else. And you need to pick your crew up again. Which can go several ways:
1. You're very lucky. Your crew was picked up by legal search and rescue operations and now is in System X at Station Y. Travel there, pay the rescue fee (costing as much as a new crew member of this experience level would cost to recruit) and you're good to go.
2. You're still lucky. Your crew was picked up by some legal operation. Same setup, travel to System X, Station Y. But the rescuer wants a service in return. Probably a cargo delivery mission, but possibly also an assassination mission of medium difficulty.
3. You're less lucky. Your crew was picked up by some shady people. But they offer to return him/her after you did a bit of work for them. Queue a chain of smuggling missions and/or assassination missions.
4. You're really unlucky. Slavers got your crew. Luckily somebody sends you a "donation" mission. If you complete that one, you get information when and where the slavers move our crew to another system. Bring your interdictor and hatch breaker.
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For scenario 3, the snitch part of szenario 4 can also happen. So when the player is just getting into dirty stuff (maybe after the first smuggling run), he gets the above mentioned "donation" mission, followed up by the "rescue from cargo hold" mission.
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Voilá! Gameplay! Crew would still be removed from the crew for a while, but people can recover them. By using nothing else but the already existing mission system. All it needs are some more text messages when the missions are sent to the player. It would add so much to the game while needing only little additional work, as all puzzle pieces are already implemented!
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