As for improving fleet AA, I would like it to be consistent and minimize change. The first thing is to simply increase AA capability (Glory does this with a research bump in AA for HFs, maybe it could be larger). Hitting AA=4 for fleets is a big difference from AA=3. For consistency, the best thing would seem to be that if the number of naval vessels is more than twice the number of attacking air, the AA gets a bonus like land flak does in the same condition. IMO, this would be a huge change making land based air a lot less effective in places like the Med, where I usually see just a couple of air units supporting the navies.
I would not propose this; as you note it would give a huge and unwarranted boost to all ship AA. What I did have in mind was to treat upgraded vessels like land-based AA. During the war there was a quantum shift in AA firepower that's not well represented by a 1 point increase in the combat rating; this allowed mid/late war vessels to function as dedicated AA platforms.
How about this. It will be easier to code, and is largely the same.
1. Unique targeting of naval (non-transport) units by CAG.
2. Once all naval (no-transport) units are covered by CAGs, independent selection using the normal (weighted) CAG probabilities.
This seems a reasonable compromise. Two questions; in step one does the unique targeting still give priority to CVs? And, what about non-CAG targeting?