As people have already stated, the current system of 2 total points being awarded in some games (regulation) and 3 total points being awarded (OT or Shootout) completely throws the balance of the standings off. There should be a predetermined amount of points up for grabs for all games, not 2 for some and 3 for others.
And on that note, I say get rid of the point system all together. The only reason NHL has a 'points' system is that historically, there had always been the possibility of a tie and those ties needed some value associated with them for the standings to 'make sense.'
Now that a tie is no longer possible, why do we even have "points"? A Win should be a Win, and a Loss should be a Loss, regardless of how the game was decided. At the end of the season, just go by winning percentage to decide the standings, just like MLB.
I also don't agree with the shootout. Is a baseball game decided by a homerun derby? No, that would be equally ridiculous. I have been a proponent of 20 minute periods until a goal is scored (as is done in the playoffs). The fact that the rules/structure of the game is completely different in the playoffs than it is in the regular season has always seemed silly to me. I think that's a topic for a different thread though as I think this is supposed to purely be about point allotment.