First, I'd like to come out and say that I value story and gameplay over graphics.  I am also a huge fan of classic games and I don't hesitate to go back and play the old computer games still in my collection.  My problem with the early 3d graphics is that they didn't age well.  The graphics were ugly then and they are even worse now.   They are at the point where no matter the story or the gameplay, I just can't get past the graphics.  The classic 2D games, such as Baldur's Gate, Icewind Dale, Planescape, and Diablo, have aged much better in my opinion and are still very playable to this day.  In fact, I am still in the middle of another playthrough of Baldur's Gate 2 right now.   Whereas, no matter how much I enjoyed playing Final Fantasy 7 when it came out (it was directly responsible for my terrible grades in the first semester of my sophmore year in high school) I can't think of going back to play it now.  The graphics are just that ugly. 
 
Give me late 2D graphics over early 3D graphics any day of the week.  Anyone else feel this way?