I do agree with sigoroth about power level; assault boats should not be as destructive as bombers, ever. However, I diverge in opinion with regards to their overall utility. Assault boats should be a viable alternative, just not in damage output. Assault boats should be good in a variety of roles, just not as many. Consider the following two possibilities:
1) Fighter Supression: With turrets suppresed, it is easy to imagine that an assault boat could board closer to its intended target, maximizing its utility and allowing it to attack more vulnerable points. Assault boats could benefit from supression, either by adding +1 to the result (allowing results past six) per fighter OR allowing a reroll of the critical result (making them more reliable).
2) Fighter resilience: IN have vanilla ordnance, and a shark assault boat has over two and a half times the armor of a fury interceptor, along with the same engine strength and almost three and a half times the directional firepower of a bomber. Other races have (presumably) even better assault boats. What if assault boats count as resilient ordnance? You could give them a weaker save (5+ or even 6+) to allow them a chance of surviving fighter interception.
In either of these cases, although bombers are capable of much greater havoc and are more lethal, a-boats are more reliable and more effective at extreme range, sort of like batteries vs. lances. I am not saying these are rules that necessarily should be implemented, just that these are oversights that the current rules don't cover, explaining the general lackluster nature of a-boats. As for SM domination, losing an attack rating point to gain thunderhawk annihilators is quite worth to the ordnance heavy SM fleet.