This seems like a decent idea of what to want in a game within the last 3-4 generations but from that point on game play is the thing that matters the most. Story is something that has just recently been getting better and atmosphere has been getting slowly better. Zombies ate your Neighbors? why? who cares just have fun. Robotniks being a prick? Take him down. Princess is in another castle? Okay, why not send me to the right one in the first place...?
I'm not discrediting two of the three points more just happy that we have gotten to this point when we can talk about those. As I also realize what we've gone from. Side note: who says Metroid Prime has no story? I've never heard that criticism about the game.