The destruction of 2D franchises, though tragic, came along with a lot of innovation; you gotta take the good and the bad.
I'm going to lay down a marker and say that no 3D adventure game added any good innovation, period. Grim Fandango is a great game, but that's despite its awful tank-control "innovation," not because of it. And the rest all were lousy and added nothing. The 3D Contra game on Playstation was terrible, too.
Since 2003-2004 things stagnated; from 2007 up until recently it drastically declined. Things have gotten noticeably better in the past few years, but the industry isn't by any means healthy.
That's craziness. You can't look upon the ruin of one man's pet genre and sing the themesong to The Facts of Life and then turn to your own pet genre and act like all change is bad change. There have been VAST innovations in RPGs: quest compasses, walkthroughs incorporated in the form of journals, difficulty rebalancing to invite in all players, ubiquitous romances of every conceivable variety, action-based combat in lieu of turn-based combat, real-time spell effects that cover the whole screen, etc., etc. Most players love that stuff. We don't. But I also don't like the crap that was done to my 2D franchises, even though there was "innovation" that allowed Super Mario World to become Super Mario Galaxy and Super Metroid to become Metroid Prime and Megaman to become Mighty Number 9 and so on. :/