I don't think a mod can do this. But it would be VERY nice to have, still.
I have been craving to create real battleships, with weapons BATTERIES. Where researching weapon techs means you can also build smaller variants that do less damage, so you can spread out more weapons mounts over your large hulls.
Basically, your tracking system (large guns track too slowly to effectively fight small, agile craft) could be implemented based on the weapon size, and would, of course, require smaller weapons (doing less damage) that would not suffer this targeting disadvantage.
It would add more weaknesses to craft. You could choose to build "fighter killers" equipped with small gun batteries, but that would hardly ever pierce the defenses of a big ship.
You could build Capship killers (Homeworld Ion Frigates, anyone?) that would sport a small set of big guns (similar to how it is now) but would be vulnerable to small enemy craft that would be hard to target with these bigger guns.
I also very much love the idea of carrier ships. Your concept of docking modules is very nice. To be able to carry 2 small or 4 tiny fighters per module would be truly great - but I don't see this coming before GalCiv3, if at all.
A problem with the gun thing alone is, there is no "miss" right now. Gunfire always hits, it simply does no damage if the defense roll is better than the attack roll. Of course, the attack roll (or the defense roll, or both) could be modified by hull size, so that larger ships firing at smaller ships would be at a disadvantage, while smaller ships attacking larger ships would suffer no such modifier.
For example, an easy way would be to subtract 20% from the attack value for each difference in hull size, i.e. a huge ship would only have 80% attack power against a large ship, 60% against medium, 40% against small, and 20% against tiny. You'd require lots of gunpower OR smaller ships to get rid of fighter craft, which in part would offset the much higher cost of said fighter craft (weapons and defense prices should also possibly be modified by the hull size, making them cheaper on smaller hulls).
This way, even the modest defenses available on small craft would allow for reasonable survivability, and make them worthwhile, tactically.