Youre on the right track - assuming that onEnterFrame is triggered in some way by Event.ENTER_FRAME - instead of skipping update, call it on every frame but pass in the time elapsed:
private function onEnterFrame() {
var now = new Date().getTime();
var delta = now - _lastTime;
_lastTime = now;
updateGameState(delta/1000);//divide by 1000 to give time in seconds
}
In updateGameState, you can utilise 'delta' to calculate movement etc, eg:
function updateGameState(timeElapsed:Number):void {
myAlien.x += myAlienSpeedPerSecond*timeElapsed;
}
This way you get smooth movement even when frame rate varies.