Actually, the plastic works fine. And, I keep the ammo with the pistol in the same case -- just insure that the pistol is unloaded (Delta's policy only allows one gun case in your checked baggage -- with up to two pistols and 11 lbs. of ammunition). Ammunition should be carried in it's retail packaging.
Usually, I take the P-3AT with one box of ammunition. In colder weather, when concealability for larger weapons is easier -- the P-3AT is carried along with my HK P7.
Of all the times I have flown with a firearm, I have only had serious difficulty with the gate agents one time -- in Tampa, shortly after 9/11. To make things easier, I now carry a printed copy of Delta's firearm policy and a copy of the TSA's policy/guidelines for the transportation of firearms on commercial aircraft in my briefcase. At times, there have been questions with inexperienced airline personnel -- having the written policy in hand made resolution easier.