there's no way a shoot out win should be worth as much as a regulation win, an ot win maybe, because the whole team is still playing, but a shoot out is not and should not be worth the same. All games should be worth the same if you're going to make all wins worth 2 points, then you have to get rid of the shoot out and no point is awarded to the losing team, but the better solution is make all games 3 point games, that only makes sense.
Here's a website that refigures the NHL standings based on various point systems, including the 3 point system, used in the Olympics.
http://www.hockeystandings.info/
The point system used can affect the playoff pairings, and in one case currently even the Presidient's Trophy leader. However, the 4 division leaders remain in first place for almost any system used.
It's interesting how a subjective decision can affect playoff seeding, and therefore the match-ups. I would hope that a decision could be made and stuck with for a long time. Historically, a team hitting 100 pts was really good. My guess why the NHL doesn't go to a 3pt system is because you'd see more than just 3 or 4 teams hitting the 100pt mark, thus devaluing the greatness of the achievment. This season 7 teams are on pace to hit the century mark. The President's Trophy winner on a 3pt system would have over 150pts.
I read an article recently that the NHL was concerned that the 5 minute overtime wasn't producing the results they wanted. 40% of overtime games went to shootouts since its inception. Tinkering with the point value of an OT win vs a shootout win was discussed to create an incentive, but won't likely get approved. The article said that the most likely thing is for the goalies to switch ends like it is in the 2nd period. The longer distance for a line change may create the plus one difference in men for a score.
I'm curious if any fan poll has been done on point systems.