I think there's no reason for now to abandon traditional buttons and the only one who's even attempting that is MS. The Wii works perfectly fine for FPSes.
As for "waggle", how about immersion? In Onslaught you have to make movements with your hand to have your character wipe his visor, throw a grenade he's holding, swing the beam whip or reload his gun. The gestures are perfectly natural and I can hadly imagine reloading in any way other than simply making a snappy movement with the remote (whatever gesture I prefer, e.g. a flicking motion like Serious Sam does with his colts or just lifting the remote up like the character does in the reload animation).