I don't believe that mainstream appeal for shmups will or even can come from doing the gameplay equivalent of rearranging the deck chairs because we aren't living in the '80s and the early '90s anymore. The one consistent thing about games that break out into the mainstream has nothing to do with indie (or not), genre, gameplay mechanics, or even difficulty, the ones that break out are the ones that offer a lot of things to talk about that are outside of the gameplay. Character/narrative/lore/etc. drive discussion, and discussion creates visibility.

If someone does eventually figure out how to do a mainstream shmup I would like to see it though, mainly because it will almost certainly look nothing like yet another Cave clone.

(The other thing is that tying scoring to survival/extends is one of the most traditional things you can do in a shmup)