Before answering this question, we ought to recall what aging well or badly means. Deus Ex vs. Invisible War is not a fair comparison because IW was vastly inferior at the time of release, and it is inferior now. It's not a question of aging then but quality. The games we are looking for should be the ones that were thought to be of similar quality at the time of release, or that the sequel was thought to be an improvement.
Therefore I nominate Fallout 2. I recently completed FO1 and was very impressed with how well-rounded and almost flawless it was in its own right. Excellent plot, probably the best world building of all time, good cast, at the times brilliant writing/acting ("You saved us, but you'll kill us. You are a hero, and you have to leave"). Holy fucking shit what an ending! I could go on, only the combat AI is a blemish to its greatness (IMO for the game to be 100% perfect you should be able to control the companions and redesign the battles to be appropriately tactical). When Fallout 2 was released, in a way it was an improvement. They really improved companions in every way, did some other QoL improvements, added shit ton of content, which improved the sandbox appeal. You had more weapons, some beefed up skills and even you own car. New Reno with its brilliant quest design is still one of the best rpg cities ever created. It had everything you could ask of a sequel to a brilliant game. I remember the game was very well received, except for the game breaking bugs and some concern for the "black humor".
Well if you play it now, it's still great but the tone is just off. FO1s has subtle humor but the shit is real, let me tell you. It's funny at the times but actually quite serious for the most part. In a way it's a bit like Conan the Barbarian, I don't ever let anyone tell me that it is just a stupid movie. Regarding Fallout 1, only Loxley character with the stupid accent sort of crosses the line to dumbfuckery. FO2 on the other had jumps over that line gleefully. The everpresent pop-culture references, that are dated to boot, are so in your face, that playing the game becomes jarring. Some of them are also CRITICAL TO THE PLOT and so you can't avoid them. As for writing, compare the caricature of stupid politicians and jingoist Americans of the Enclave to the character of overseer: one is juvenile and reflecting the simplistic anti-establishment political views of the author and the other one is funny, subtle, and even a bit thought provoking. Many of this stuff we didn't mind when we were playing it the first time, because we were engrossed in playing through the excellent new content. Another important factor was that most, even majority, of the people playing the game at the time of release were teens or even pre-teens. What was funny to them then, isn't funny now. People mature, but the game stays the same.
Fallout 1 was a mature game to begin with. It's amazing how diligently it executes its concept. Everything is balanced from systems to quest design to world building to art direction to plot to writing. It's one of those few games that is just marvel to behold, it just works. When you play Fallout 2 on the other hand, you enjoy it, but keep wondering what could have been. What if it had no pop-culture references? What if the villains weren't so cartoony? What if it didn't have Tom Cruise? What if it it was just one notch darker and just a tiny bit more serious? It's not even too much to ask, as the step you keep thinking about is so small. Most of the time Fallout 2 succeeds in what it tries, and at the times it even surpasses Fallout 1. But that makes the failures even more apparent. Comparing these two brilliant crpgs truly makes a case for "less is more".