Maybe they do, but are today's graphics and sound really superior? Its impossible to argue that the hardware isn't superior, but that doesn't mean the things created with it are.
I can easily see calling Doom superior to pretty much most FPSes today. Half-Life and Red Faction and Halo were good for what they were but they're just not the greatest. The main thing is that those are games you kinda have to dedicate yourself to, whereas Doom you can just load it up, play a level and be done with it.
Depending on how you define 3D, I'd say yeah.I think the real debate here is - are 2D games better than 3D ones...
One of the big reasons IMO is just that 3D games drag. Using your own LTTP versus 3D Zeldas... in Link to the Past, you can get from point A to Point B in Hyrule, by foot, in under five minutes. In Ocarina of Time you can get from point A to point B in five minutes... if you're at Hyrule Castle and Point B is LonLon Ranch, and you have Epona, and she doesn't get hung up on any fences or anything when you whistle for her. Camera is also an issue that 2D never had.
I wrote a bigger list of reasons once, but it needs some re-thinking. In general though I find I always prefer 2D over 3D.