In my game I house-ruled "gun AC" to be the average of normal AC and touch AC, and made that apply at all ranges for firearms (so a dragon 5 ft past the first range increment wouldn't suddenly gain +30 AC, for example). Basically, armor and natural armor had half normal effect. I feel this is a fair adjustment since most gun-users are at a +1 BAB/level progression so they should have good enough attack rolls that this is not a hardship. I also invented a "ballistic" armor/shield property that allows the item to count all its AC bonus for gun AC, so martial artists don't get to have ALL the fun. Some called this "too much math", but in my opinion no more so than figuring things like CMB and CMD (should I mention I also house-rule CMD to only use max[str, dex] rather than [str + dex], so mid-to-high level combat maneuvers may still succeed?).
Others have suggested using flat-footed AC rather than touch AC, to represent armor working against firearms but not dodging. This is probably okay for a campaign where guns are rare and primitive (primitive -> armor works, rare -> people can't dodge guns or don't because they don't know what they are). Perhaps a feats or class abilities can restore half or all the AC, analogous to that "ballistic" property.