How about a new ship type? Guerilla Cache, or somesuch. Low cap. Cloaking. Tractor beams? Transports up to XX units that no longer count towards their cap while inside the transport, but the Cache cannot be unloaded for XX minutes after loading. Automatically unloads when enemies are present, unless in stand-down mode.
Basically packing some units away as a just-in-case emergency thing to crack open when needed, or as a sort of special trap.
Might be a stupid idea.