I just came about the proposed 5.7 changes today, and realized that Steve is about to consolidate engine and missile-engine design to one process for consistency reasons. Importantly, he also announced economies-of-scale effects for ship engines, such that a larger ship engine is (slightly) more fuel-efficient than a smaller ship engine.
If that principle also gets applied to missile engines, and is sufficiently large, it could go a long way to solve our problem. Right now, most missile characteristics are independent of the size (range, speed, total damage, hit chances), but under the proposed changes that could change markedly. If a size-1 missile could not host enough fuel to reach normal combat ranges then large missiles would be viable choice and in turn AMM would make sense again.
Right now, it seems as though size-1s are a dominant strategy, and AMMs are a loosing strategy (unless one assumes a consistently suboptimal enemy - which the NPRs can be - or maybe PDCs).