The scoring method was by far the fairest method possible and prevented the chance for one lone game with only one individual vote in it's name to storm the list because it was considered one persons favourite game.
The fact the list wasn't finished before the Wii U is due to the staff having to work on other things. Sign up as a staff member if you would like to help them out in future, I'm sure they could use all the help.
Regarding Metroid it was the only fair way. Members themselves couldn't decide during the 3 weeks so it was done this fair way. Besides, I'd imagine very few people have actually played the Metroid Prime Trilogy, and instead played each game indivually when they were released. I don't think it's right that people vote for a game they haven't played, whatever its quality, as it would completely change the purpose of the list.