The whole point of auto-shot is that it's uncontrolled; you pull the trigger three times and hope for the best. The payoff is that you get up to three hits at a reduced TU cost and, rather more importantly, the enemy doesn't get a chance at reaction fire until you're done. I consider that more then an even trade, in fact I use this firing mode near-exclusively because odds are just about always in favour at least one of the shots will hit something at any range.
Though Volutar's point about aliens instantly dropping is valid (even if it'd be quite a game changer to leave them standing), I also use Daiky's tactic of attempting to take out a group of aliens with one auto-shot (just about every time I breach a medium scout for eg).