The thing is, I don't really think that the possibility of a game over adds any real risk, at least not if implemented as in Banjo-Kazooie or the 3D Super Mario games. You don't actually loose anything of importance in-game, all that happens is that you have travel through the hub world to get back to the level, and if the game has check-points, you loose your check-point, so you have to play through some of the level again. That's just the game wasting the players time, and a good game should never waste a players time. That's something free-to-play games does to try to get you to spend money.
I'm perfectly fine with making death meaningful, but adding lives doesn't necessarily do that. The notes resetting in Banjo-Kazooie, as you also mentioned, is a perfect example of a way to make death meaningful. That's what I'd like to see: A new and interesting way of making death meaningful instead of just another game with lives.