One vote each is boring and sometimes we only get 6-7 voters. With two votes, even if you "favorite" doesn't get first, it will still be one of the favorites of the site that the most people liked. I don't think any value for the winner is lost at all. It is simply a popularity contest for those subs that the most people like the most.
Look at it this way. If 4 people all like different submissions as their top favorite #1 but then all like a second place "not the greatest" post as a good second choice, then I would rather give the 1st place award "second place" vote the win because it appealed to the most people.
So, in my mind, you can argue that "first place" may not win "first place" but when a single submission gets the most "likes" than any other, then it has the best cross taste appeal and therefore the best quest sub whether or not it is your favorite. At least that is something of my reasoning.
(PS, I also have enough bugs and features I need to fix/implement without an entire new voting systems too.

We need to work inside the confines of what the system comes with in this case. )
ON ANOTHER NOTE!!
Chaosmark sponsored prizes for this quest!!
First Place: Your choice of a Gem Dice set from -
http://www.gamescience.com/gemrole-playingsetsSecond Place: Your choice of an Opaque Dice set from -
http://www.gamescience.com/opaquerole-playingdiceSee this post and view the videos to understand their awesomeness!!
http://strolen.com/guild/index.php/topic,424.msg71233.html#msg71233Thanks Chaos!!!