How about a small specialized warhead for targetting other missiles. A reasearch cost of 5-10000 rp and the effect of getting a minimum size warhead doing less than 1 point of damage (ie gauss weapons) The benifit being a flat 5-10% improvement on the final chance to intercept another missile
In v3.0, warhead strengths are doubled and you can design missiles based on 1/4 MSP increments, which makes building small anti-missiles a lot easier. To get the increased chance to hit, add some MSP devoted to agility or extra speed.
Steve