While I am not particularly fond of the hookshot or the flippers there is currently nothing in the rules against using them or removing NES items from being accessible in the quest. Are you suggesting we add that to the rules?
While I think adding a screen for DN is a great idea, I don't think we should force it on entrants. I like what c-a-d said about using DarkNation or DN to access the quest or maybe DarkN.
I like the idea of a hybrid system of dedicated judges and community voting(which you know because I suggested just such a method to you in chat). Maybe we could merge the two ideas. Each judge awarding their choice a point and each category in community poll awards. Quest with most points wins.