Well I must agree that you do have a point here. Difference between most new 3D games and the ones you mentioned is the quality of play. The games were innovative and not just some product following other games in a neat straight line (Well not most of them now).
There are some new 3D games which I have enjoyed myself, but they lose their charm too quickly for my taste. Instead of concentrating on making a great game the team instead concentrates on the graphics with 3D engine and effects. Of course I know most gamers will probably hate the game if it isn't able to give out good graphics, but all this attention to the graphics and effects make them forget that they should make games which aren't just spinoffs of other games. Doom was a copy of Wolfenstein and since then it's been going that way mostly. Usually it's shoot anything that moves. Then some bright guy thought of adding people whom you should not shoot (Well whom you don't NEED to shoot) and there have also been other new effects, but essentially the 3D shooters are basically still the same game with slightly improved effects and usually a disturbing lack of quality and creativity.
The same for most other games which use 3D like some RTS games. Of course it might look great that you have all the control of the view, but still if they had proper graphics artists the games would look much better than some of their attempts at making 3D rendered figures.
Some people tend to think that all game categories possible have been invented. I think they're wrong. All it takes is a guy with a good idea to create a new gametype. This could be 3D or good old 2D graphics, but to be able to market the game you'd need to have good graphics and to many people good graphics mean 3D acceleration. 3D acceleration can save a lot of work if you just have a talented artist to make 3D models and skins, but if you were able to do it 2D you'd have more control of what it looks like in the game and it would be a lot less demanding on the system leaving more resources to the actual gameplay in the case that it's demanding.
I don't hate 3D as such, I just think it's sad to see everyone hop on the 3D bandwagon and think that if they can just produce enough eyecandy gameplay and inventiveness doesn't matter a bit. It's even worse that the majority of consumers don't really mind as long as it looks good.