It seems to be fairly well accepted that the dominant strategy in Aurora is using lots of very small missiles. There are a few downsides, but at the end of the day, most battles come down to overwhelming the enemy's point defence and the way to do that is with lots small missiles. In the general spirit of balance, I propose a simple nerf. Make missile engines less efficient.
At present, missile engine efficiency is really a bit of a joke. With a TN start and automatically assigned RP, a size 50 res 1 sensor will spot an incoming missile at 5m km. At the same tech level, a size 1 missile with 0. 01 (1% of total size) devoted to fuel will have a range of 6m km. Devoting 10% of total size gives you a multipurpose anti-ship and anti-missile, with only a minor cost to performance.
By making missiles (especially small missiles) more fuel hungry, the efficiency bonuses conferred by larger engines will start to make an impact and we'll have to make real tradeoffs between range and quantity.