Big, slow missiles will be easier to shoot down. Armoured missiles were removed because they were too good. . . at least against the computer. Hopefully Aurora's AIs will improve to the point where we can have them back.*
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*Because I would like missiles to function properly in nebulae (which, for the record, are also gone from 1.0 C# Aurora) -- which means non-armoured missiles are detroyed immediately upon launch, and armoured missiles have their speeds properly reduced by the nebula like ships do.