Before I give names, I'd like to express a few thoughts:
-If a game has aged well, that might be because what was good about it then still holds today.
-If it has not, it is possibly because it was only relatively good, and its virtues were thus sort of flash-in-the-pan; More people saw The Ten Commandments than John Cassavetes' Shadows in 1958, but Shadows has had the longer lasting influence.
-I will not say a game aged poorly if it was lousy when it first came out. I will say it was always lousy, and though time may further exaggerate its flaws, it has not lost something that it had.
-These judgments are only subjective opinions. Where I state anything objective, it is either conjectural, or noting something that has influenced my opinion in a meaningful way.
-I only use games that I liked a little or a lot when they first came out or I first saw them, because age has in some sense changed my judgment.
In that vein, I offer up the following list of games that I think have aged poorly:
-Final Fantasy IV-IX: Largely due to problems completely beyond possibility of remedy at the time, these six games are lost in what will someday perhaps be known as video gaming's 'silent era' (as critics are excessively fond of comparing games to movies now, I think the terminology inevitable) and appreciating them on their own terms will be mainly for those who were there when they first came along. For the rest, it will be done with an outsider's eye, with attention more to the history of art than the art itself. Playing even isolated snippets of it will be more like watching D.W. Griffith's Intolerance than a contemporary movie. Someday, students will play/see and need scholarly presentation in seeing the influence and growth at work.
-Wolfenstein 3D: Will be remembered as a propaedeutic to Doom and the FPS genre, but its own virtues will go largely unmentioned, I suspect.
-Doom 3: It felt like an expensively rehashed Doom without everything that interests the gamer so easily there. The level design feels as if the designers at id had not noticed or imagined a way the genre might move forward in the 10 years since Doom came along, and had no inkling of the contributions of System Shock, System Shock 2, Half-Life, or any of the other games that took the genre to new places. The interface, which was delightfully slick, is another story. This is not to be misunderstood; Doom 3 is a tech demo for a then state-of-the-art new game engine. I am not saying it is a bad game. I had lots of fun playing it, and would still if I did play through it again today. But it doesn't feel as monumental as it did then, and time will further diminish it.
-Age of Mythology: As a simple matter of visuals, its graphics show age more readily than Age I or II, though I am ill-equipped to define how this is so.
-Soldier of Fortune: Its approach to violence was bold and original, but its visuals lack the impact they had then.