I think multiple AA shots might work if the maximum kills were limited in some way. A few triple-roll AA cruisers might be too much – say max the kill-rate at one plane/cruiser regardless of the number of AA dice rolled? But I think there are more issues that need some thought…
Cruisers were only more effective than destroyers for AA kills. Cruisers certainly had less AA than carriers (CVEs excluded) or battleships but far more than destroyers. Late-war US Navy stats (non-suicide) show a fairly consistent 17% - 24% of plane attacks were shot down by AA regardless of ship type. Although one fast-carrier group shot down as many as 33% (but that is a high). Generally, battleships, carriers and cruisers shot down the same percentage of aircraft while destroyers averaged a little better than half that rate. These are late-war stats with increased AA mounts, improved directors, radar, mechanical computers and VT fuses against a desperate, poorly trained enemy. AA rules allowing more than 33% AA kill rate might be pushing the envelope. Three dice is a lot.
I’d believe it if AA shots were given to carriers and battleships but that doesn’t do much for cruisers. Cruisers were far easier and faster to build than capital ships. Battleships were exponentially more powerful (attack and defense) and also exponentially more expensive and difficult to build than cruisers and there-in lies the problem. Thus the 6 cruisers to 1 battleship production rate mentioned earlier.
2 cruisers will statistically beat 1 battleship in both Global 1940 combat rules and IPC cost BUT tonnage-wise 3 heavy cruisers = one battleship (15,000 CA vs 45000 BB). And Light cruisers were half the tonnage of heavy cruisers (7000 CL vs 15000 CA) so that makes things even worse when averaging things (I’m using general numbers here, there are extreme examples on either side).
In the real world 3 cruisers would only blind a battleship on a good day, possibly sinking it if they had torpedoes and got lucky. The Battle of the River Plate shows just how dangerous even one small Battle Cruiser can be versus cruisers at 1 to 3 odds. I think Battleships need more power but with limited production rules. Give them double dice rolls to hit with both dice counting but force production over two turns while increasing their cost. That might be more realistic (can I say that in Axis and Allies?
) AND perhaps give cruisers a proper place.
No ship, no pair of ships could dare equal the mighty Battleship – it took an airplane to beat it. Well…, excepting a pair of submarines but that’s another story. 
I think there needs to be an adjustment to make the cruiser useful in this game or simply drop it. Just my thoughts.