How about this:
At the start of each Invasion Mode mission, one of the stations starts out with a very limited supply of homing, mine, EMP, and nuke torpedoes. That station notifies the players that is is expecting a transport to reach the sector in (random number) minutes.
After (random number) minutes the transport spawns on the map edge, but an extra Skaraan also spawns with its AI set to favor killing transports.
The transport will NOT respond to Comms orders until after it arrives at its destination. If the destination station is destroyed before the transport arrives then this condition is voided and the players can divert the transport to another station.
Once the transport successfully arrives at its destination, that station receives a treasure trove of torpedoes. In effect, the most undesirable station suddenly becomes the most desirable station.
Thereafter the empty transport is useful as bait. Enemies may chase it.
"Damn the torpedoes! Four bells, Captain Drayton!"
(Likely actual words of Admiral David Farragut, USN, at the battle of Mobile Bay. Four bells was the signal for the engine room to make full steam ahead).