I think a lot of this "oh where has all the originality gone" is euphoric recall. How many times do you think "I'll have a look at such-and-such", get excited at the prospect then quickly recall 3-minute intros you couldn't skip past, poor or non-existant logic and AI, saves to floppy only, games that do not use expanded memory and so forth (not all cases I know).
I certainly think title like Tomb Raider were excellent, utilising 3D itself to make the puzzles ingenious, I recall one scenario where activating a lever rotated a whole game environment 90 degrees and so on, maximising use of the layout. Likewise Jak n Daxter and similar are excellent. Then there is the Resident Evil series, the Silent Hill series ... etc... The latest Final Fantasy series games are 3D only in as much as the backgrounds are now polygon built, were they prerendered instead they would be pretty much a "2D game" also.
I don't necessarily think "3D = bad", time moves on and the customer expects 3D where it is possible. So what? Rate the games on individual merit.
It's as if people "remember" a Golden Age (maybe that should be a Golden Axe?) wherein ALL games were superb, without exception. Go download a stack of games assuming you are without pre-existing knowledge from back2roots or similar, they'll be 80% garbage just like nowadays.
Good games are good games irrespective of 2D versus 3D. You can't polish a turd.