Missiles
... In addition to the reduced range it should also adjust the to-hit chance in the same manor beam fire control chances are reduced.
IMO it should be either/or. If you like reduced range, leave it at that (and/or affect beam range instead of beam accuracy). If you'd rather reduce the hit chance, then don't reduce the range.
Smallcraft
... smallcraft only have levels 1-6.
Nitpick: I think it's 1-5, actually.
Instead the should be dependent on the second level of full size ship systems and either Gunboat or Fighter engine developement for introduction and stay 1 level behind the full size systems in the same manor as compact systems(but not dependent on them).
That would render compact levels 1-5 mostly obsolete. I'd prefer 1 level behind the compact systems. In essence, miniaturization level 2 requires miniaturization level 1 (i.e. compact before supercompact for "small craft").
ECCM
ECCM is more of a long term suggestion. Take if from being a seperate system that is assigned to a fire control and make it a component of the fire control. But, it should not be a required component.
I like this. Sure, it makes it different from ECM, but it also jives better with the built-in ECCM of CIWS.