I was thinking about this as a good missile boat build:
Colonel Jendon + STS-321 + Saboteur + Ion Cannon (34)
Major Rhymer + Advanced Proton Torpedoes + Cluster Missiles (36)
Captain Jonus + Concussion Missiles + Cluster Missiles (30)
Total: 100
With the Shuttle packing the STS-321 upgrade, I could afford to hang back really far until turn one and two pass, passing target locks onto my bombers, then throttle up and let them have it with APT and clusters, then the concussion missiles. The shuttle's ion cannon can disable one of the ships, allowing the bombers to concentrate on it, then finish off whatever's left with the bombers' laser cannons.
I think this would be a great list to take against HSF, though it might run into trouble against any list with the A-wing or X-wing unless I flew really well. Both of them could cause major trouble for the shuttle, and the X-wing would be ideal against the bomber, unless I took them out early as they tried to run past me. A single missile would spell trouble for the X-wing, and if I could get a hit with the APT or ion cannon an A-wing would be toast (unless we're talking bad rolls here).
Thoughts?