I've read the changes list over time, but I think I might be missing something. Has size 1 missile (abuse) spam been mitigated. It seems like missiles are generally going to be slower and/or shorter range, but I'm not sure that addresses excessive size 1 spam.
You will eventually need to use electronics in them in order for them to be accurate, this will make them bigger in general. You are likely to use AMM at 1-2 in size for this reason.
Small missiles will probably have quite restrictive range as ASM as you will need allot of electronics in them now and smaller engines are less fuel efficient than before, especially with a high power setting. If the yield in them is too small you can also begin absorbing some of them on your passive defenses such as shields etc... this is something many don't consider as a viable way to combat missiles. You are not forced to stop them all, just enough to not hurt you too much.
These factors should make missiles grow relatively large in comparison to how they were designed before.
Although you will need a decent tech level before electronics is usable. The way I see it the first two levels and ECM and ECCM rarely make them better, rather worse in many cases. At 20% I think it is a toss up if they are usable or not, in some circumstances they perhaps is usable in others not so much. I think these techs should start at 20% and not 10%... the first level could be more expensive as a compensation.
I could see that you perhaps want to have both slower long range missiles and shorter ranged faster missiles against enemy ships, they would probably both serve a purpose in the game. You could also want larger missiles with smaller sub munition missiles (MIRV). But they have their own problems since they are very slow and subject to be intercepted before the sub munition is released.